Load ncbi (6.1.20031028) into ncbi-tools6/branches/upstream/current.

319 files changed, 29045 insertions, 275 deletions

diff --git a/network/blast3/client/.NETBLAST_VERSION b/network/blast3/client/.NETBLAST_VERSION
new file mode 100644
index 00000000..bda8fbec
--- /dev/null
+++ b/network/blast3/client/.NETBLAST_VERSION
@@ -0,0 +1 @@
+2.2.6
diff --git a/network/id1arch/id1.asn b/network/id1arch/id1.asn
index 7f8d3cc1..8968c13b 100644
--- a/network/id1arch/id1.asn
+++ b/network/id1arch/id1.asn
@@ -1,4 +1,4 @@
---$Revision: 1.9 $
+--$Revision: 1.12 $
 --********************************************************************
 --
 --  Network Id server network access
@@ -47,10 +47,10 @@ ID1server-maxcomplex ::= SEQUENCE {
 }
 
 Entry-complexities ::= INTEGER {
-		entry (0) ,             -- the "natural" entry for this (nuc-prot) 
-		bioseq (1) ,            -- only the bioseq identified
-		bioseq-set (2) ,        -- any seg-set it may be part of
-		nuc-prot (3) ,            -- any nuc-prot it may be part of
+		entry (0) ,              -- the "natural" entry for this (nuc-prot) 
+		bioseq (1) ,             -- only the bioseq identified
+		bioseq-set (2) ,         -- any seg-set it may be part of
+		nuc-prot (3) ,           -- any nuc-prot it may be part of
 		pub-set (4) 
 }
 
@@ -86,6 +86,9 @@ ID1blob-info ::= SEQUENCE {
 		suppress	INTEGER,
 		withdrawn	INTEGER,
 		confidential	INTEGER,
+                -- blob-state now contains blob version info.
+                -- it's actually minutes from 01/01/1970
+                -- and it's negative if blob is dead.
 		blob-state	INTEGER,
                 comment         VisibleString OPTIONAL, -- public comment for withdrawn record 
 		extfeatmask	INTEGER	      OPTIONAL  -- mask for external features (SNP,...)
diff --git a/network/id1arch/id1.h b/network/id1arch/id1.h
index a9596d75..2623ca9b 100644
--- a/network/id1arch/id1.h
+++ b/network/id1arch/id1.h
@@ -9,7 +9,7 @@
 #include <asn.h>
 #endif
 
-static char * asnfilename = "id1.h18";
+static char * asnfilename = "id1.h10";
 static AsnValxNode avnx[5] = {
     {20,"entry" ,0,0.0,&avnx[1] } ,
     {20,"bioseq" ,1,0.0,&avnx[2] } ,
@@ -80,7 +80,7 @@ static AsnType atx[60] = {
   {0, NULL,1,-1,0,0,0,0,0,0,NULL,&atx[27],NULL,0,NULL} };
 
 static AsnModule ampx[1] = {
-  { "NCBI-ID1Access" , "id1.h18",&atx[0],NULL,NULL,0,0} };
+  { "NCBI-ID1Access" , "id1.h10",&atx[0],NULL,NULL,0,0} };
 
 static AsnValxNodePtr avn = avnx;
 static AsnTypePtr at = atx;
diff --git a/network/id1arch/id1gen.c b/network/id1arch/id1gen.c
index a5a2fa4f..91fac52c 100644
--- a/network/id1arch/id1gen.c
+++ b/network/id1arch/id1gen.c
@@ -32,7 +32,7 @@ id1genAsnLoad(void)
 
 /**************************************************
 *    Generated object loaders for Module NCBI-ID1Access
-*    Generated using ASNCODE Revision: 6.0 at Mar 18, 2003 12:08 PM
+*    Generated using ASNCODE Revision: 6.0 at Jul 9, 2003  4:55 PM
 *
 **************************************************/
 
diff --git a/network/id1arch/id1gen.h b/network/id1arch/id1gen.h
index f7cc4209..94c8811a 100644
--- a/network/id1arch/id1gen.h
+++ b/network/id1arch/id1gen.h
@@ -17,7 +17,7 @@ extern "C" { /* } */
 /**************************************************
 *
 *    Generated objects for Module NCBI-ID1Access
-*    Generated using ASNCODE Revision: 6.0 at Mar 18, 2003 12:08 PM
+*    Generated using ASNCODE Revision: 6.0 at Jul 9, 2003  4:55 PM
 *
 **************************************************/
 
diff --git a/network/medarch/client/mdrcherr.h b/network/medarch/client/mdrcherr.h
index 22a24985..69889082 100644
--- a/network/medarch/client/mdrcherr.h
+++ b/network/medarch/client/mdrcherr.h
@@ -3,6 +3,11 @@
 *
 * RCS Modification History:
 * $Log: mdrcherr.h,v $
+* Revision 6.1  2003/10/01 13:07:50  bazhin
+* Added a couple of new warning messages ERR_REFERENCE_NoConsortAuthors
+* and ERR_REFERENCE_DiffConsortAuthors. The severity of message
+* ERR_REFERENCE_MedlineMatchIgnored changed from WARNING to ERROR.
+*
 * Revision 6.0  1997/08/25 18:35:37  madden
 * Revision changed to 6.0
 *
@@ -29,6 +34,8 @@
 #define ERR_REFERENCE_Multiple_muid  1,6
 #define ERR_REFERENCE_MedlineMatchIgnored  1,7
 #define ERR_REFERENCE_MuidMissmatch  1,8
+#define ERR_REFERENCE_NoConsortAuthors 1,9
+#define ERR_REFERENCE_DiffConsortAuthors 1,10
 #define ERR_PRINT  2,0
 #define ERR_PRINT_Failed  2,1
 
diff --git a/network/medarch/client/medarch.msg b/network/medarch/client/medarch.msg
index 7cfa0d27..9df68937 100644
--- a/network/medarch/client/medarch.msg
+++ b/network/medarch/client/medarch.msg
@@ -6,8 +6,10 @@ $^   OldInPress, 3, SEV_WARNING
 $^   No_reference, 4, SEV_WARNING
 $^   Multiple_ref, 5, SEV_WARNING
 $^   Multiple_muid, 6, SEV_WARNING
-$^   MedlineMatchIgnored, 7, SEV_WARNING
+$^   MedlineMatchIgnored, 7, SEV_ERROR
 $^   MuidMissmatch, 8, SEV_WARNING
+$^   NoConsortAuthors, 9, SEV_WARNING
+$^   DiffConsortAuthors, 10, SEV_WARNING
 
 $$ PRINT, 2
 $^   Failed, 1, SEV_WARNING
diff --git a/network/medarch/client/medutil.c b/network/medarch/client/medutil.c
index 7914ea5e..1ebed5c2 100644
--- a/network/medarch/client/medutil.c
+++ b/network/medarch/client/medutil.c
@@ -28,7 +28,7 @@
 *   
 * Version Creation Date: 8/31/93
 *
-* $Revision: 6.8 $
+* $Revision: 6.10 $
 *
 * File Description:  Medline Utilities for MedArch
 *   Assumes user calls MedArchInit and Fini
@@ -44,6 +44,12 @@
 *
 * RCS Modification History:
 * $Log: medutil.c,v $
+* Revision 6.10  2003/10/01 13:08:33  bazhin
+* Modified ten_authors() function to handle consortiums properly.
+*
+* Revision 6.9  2003/09/10 18:47:28  bazhin
+* "print_pub()" function now is aware of consortiums.
+*
 * Revision 6.8  2003/03/25 19:14:59  bazhin
 * Function "ten_authors()" became public (from static).
 *
@@ -171,14 +177,22 @@ void print_pub(ValNodePtr pub, Boolean found, Boolean auth, Int4 muid)
 	      
 	      if (art->authors->choice == 1) {
 		 	aup = v->data.ptrvalue;
-		 	if (aup != NULL) {
-		    	namestd = aup->name->data;
-		    	if (namestd->names[0]) {
-		    		last = namestd->names[0];
-		    	}
-		    	if (namestd->names[4]) {
-		    		first = namestd->names[4];
-		    	}
+		 	if (aup != NULL)
+			{
+				if(aup->name->choice == 2)
+				{
+			    		namestd = aup->name->data;
+				    	if (namestd->names[0])
+					{
+			    			last = namestd->names[0];
+				    	}
+			    		if (namestd->names[4])
+					{
+				    		first = namestd->names[4];
+				    	}
+				}
+				else if(aup->name->choice == 5)
+					last = aup->name->data;
 		 	}
 	      } else  {
 		 	first = "";
@@ -219,7 +233,7 @@ void print_pub(ValNodePtr pub, Boolean found, Boolean auth, Int4 muid)
 		vol = "no volume number";
 	}
 	if (auth) {
-		ErrPostEx(SEV_WARNING, ERR_REFERENCE_MedlineMatchIgnored,  
+		ErrPostEx(SEV_ERROR, ERR_REFERENCE_MedlineMatchIgnored,  
     	"Too many author name differences: %ld|%s %s|%s|(%d)|%s|%s", 
     				(long) muid, last, first, s_title, (int) year, vol, page);
     	return;
@@ -248,93 +262,188 @@ void print_pub(ValNodePtr pub, Boolean found, Boolean auth, Int4 muid)
     return;
 }
 
-/*--------------------------- ten_authors() ---------------------------*/
+/**********************************************************/
+static Boolean ten_authors_compare(CitArtPtr capold, CitArtPtr capnew)
+{
+    ValNodePtr old;
+    ValNodePtr new;
+    ValNodePtr vnp;
+    CharPtr    namesnew[10];
+    Int4       numold;
+    Int4       numnew;
+    Int4       match;
+    Int4       i;
+
+    if(capold == NULL || capold->authors == NULL ||
+       capold->authors->names == NULL)
+        return(TRUE);
+    if(capnew == NULL || capnew->authors == NULL ||
+       capnew->authors->names == NULL)
+        return(FALSE);
+    if(capold->authors->choice != capnew->authors->choice ||
+       capold->authors->choice == 1)
+        return(TRUE);
+
+    old = capold->authors->names;
+    new = capnew->authors->names;
+
+    for(numnew = 0, vnp = old; vnp != NULL; vnp = vnp->next)
+        if(vnp->data.ptrvalue != NULL)
+            numnew++;
+
+    for(numold = 0, vnp = new; vnp != NULL && numold < 10; vnp = vnp->next)
+        if(vnp->data.ptrvalue != NULL)
+            namesnew[numold++] = vnp->data.ptrvalue;
+
+    for(match = 0, vnp = old; vnp != NULL; vnp = vnp->next)
+    {
+        if(vnp->data.ptrvalue == NULL)
+            continue;
+
+        for(i = 0; i < numnew; i++)
+        {
+            if(StringICmp(vnp->data.ptrvalue, namesnew[i]) == 0)
+            {
+                match++;
+                break;
+            }
+        }
+    }
 
-/****************************************************************************
-*    ten_authors   
-* 											
-****************************************************************************/
-Boolean ten_authors(CitArtPtr art, CitArtPtr art_tmp) 
+    i = (numold < numnew) ? numold : numnew;
+    if(i > 3 * match)
+        return(FALSE);
+
+    if(numold > 10)
+    {
+        AuthListFree(capnew->authors);
+        capnew->authors = capold->authors;
+        capold->authors = NULL;
+    }
+    return(TRUE);
+}
+
+/**********************************************************/
+Boolean ten_authors(CitArtPtr art, CitArtPtr art_tmp)
 {
-	Int2 num, numnew, i, match, n;
-	ValNodePtr v;
-	CharPtr ptr, mu[10];
-	AuthorPtr	aup;
-    NameStdPtr  namestd;
-    Boolean		no_compare = TRUE, ret = TRUE;
-		
-		if (art == NULL || art_tmp == NULL) {
-			return TRUE;
-		}
-		numnew = 0;
-		num = 0;
-		match = 0;
-		if (art->authors != NULL)
-		{
-			for (v = art->authors->names; v != NULL;
-									v = v->next, num++);
-		}
-		if (art_tmp->authors != NULL)
-		{
-			for (v = art_tmp->authors->names; v != NULL && numnew < 10;
-								v = v->next, numnew++) {
-				aup = v->data.ptrvalue;
-				if(aup->name->choice == 2)
-				{
-					namestd = aup->name->data;
-					mu[numnew] = namestd->names[0];
-				}
-				else if(aup->name->choice == 5)
-					mu[numnew] = aup->name->data;
-			}
-		}
+    NameStdPtr namestd;
+    ValNodePtr v;
+    AuthorPtr  aup;
+    CharPtr    mu[10];
+    CharPtr    oldcon;
+    CharPtr    newcon;
+    Int2       num;
+    Int2       numnew;
+    Int2       i;
+    Int2       match;
+
+    if(art_tmp == NULL)
+        return(FALSE);
+    if(art_tmp->authors == NULL || art_tmp->authors->names == NULL)
+    {
+        if(art != NULL && art->authors != NULL)
+        {
+            if(art_tmp->authors != NULL)
+                AuthListFree(art_tmp->authors);
+            art_tmp->authors = art->authors;
+            art->authors = NULL;
+        }
+        return(TRUE);
+    }
+    if(art == NULL || art->authors == NULL || art->authors->names == NULL ||
+       art->authors->choice != art_tmp->authors->choice)
+        return(TRUE);
+
+    if(art->authors->choice != 1)
+        return(ten_authors_compare(art, art_tmp));
+
+    oldcon = NULL;
+    for(num = 0, v = art->authors->names; v != NULL; v = v->next)
+    {
+        aup = v->data.ptrvalue;
+        if(aup->name->choice == 2)
+            num++;
+        else if(aup->name->choice == 5)
+            oldcon = aup->name->data;
+    }
 
-		if (art->authors != NULL && art_tmp->authors != NULL) {
-			if (art->authors->choice == 1 && art_tmp->authors->choice == 1) {
-				no_compare = FALSE;
-				for (v = art->authors->names; v != NULL; v = v->next) {
-					aup = v->data.ptrvalue;
-					if(aup->name->choice == 2)
-					{
-						namestd = aup->name->data;
-						ptr = namestd->names[0];
-					}
-					else if(aup->name->choice == 5)
-						ptr = aup->name->data;
-					else
-						continue;
-					for (i = 0; i < numnew; i++) {
-						if (StringICmp(ptr, mu[i]) == 0) {
-							match++;
-							break;
-						}
-					}	
-				}
-			} 
-		}
-		if (no_compare) {
-			ret = TRUE;  /* replace */
-			if (num == 0 && numnew == 0) {
-					ret = TRUE;			/* replace */
-			} else if (num == 0) {   /* no original authors - replace*/
-				ret = TRUE;
-			} else if (numnew == 0) { /* no Medline authors -  don't replace*/
-				ret = FALSE;
-			}
-		} else {
-				n = num < numnew?num:numnew;
-				if (n > 3*match) { 
-					ret = FALSE;
-				}
-		}
-		if (ret && (num > 10 || numnew == 0))     /* original article has > 10 authors */
-		{
-			AuthListFree(art_tmp->authors);  /* keep original authors */
-			art_tmp->authors = art->authors;
-			art->authors = NULL;
-		}
-		return ret;
+    for(newcon = NULL, v = art_tmp->authors->names; v != NULL; v = v->next)
+    {
+        aup = v->data.ptrvalue;
+        if(aup->name->choice == 5)
+        {
+            newcon = aup->name->data;
+            break;
+        }
+    }
+
+    if(oldcon != NULL)
+    {
+        if(newcon == NULL)
+        {
+            ErrPostEx(SEV_WARNING, ERR_REFERENCE_NoConsortAuthors,
+                      "Publication as returned by MedArch lacks consortium authors of the original publication: \"%s\".",
+                      oldcon);
+            aup = AuthorNew();
+            aup->name = PersonIdNew();
+            aup->name->choice = 5;
+            aup->name->data = StringSave(oldcon);
+            v = ValNodeNew(NULL);
+            v->data.ptrvalue = aup;
+            v->next = art_tmp->authors->names;
+            art_tmp->authors->names = v;
+            newcon = oldcon;
+        }
+        else if(StringICmp(oldcon, newcon) != 0)
+        {
+            ErrPostEx(SEV_WARNING, ERR_REFERENCE_DiffConsortAuthors,
+                      "Consortium author names differ. Original is \"%s\". MedArch's is \"%s\".",
+                      oldcon, newcon);
+        }
+        if(num == 0)
+            return(TRUE);
+    }
+
+    numnew = 0;
+    for(v = art_tmp->authors->names; v != NULL && numnew < 10; v = v->next)
+    {
+        aup = v->data.ptrvalue;
+        if(aup->name->choice != 2)
+            continue;
+        namestd = aup->name->data;
+        mu[numnew++] = namestd->names[0];
+    }
+
+    for(match = 0, v = art->authors->names; v != NULL; v = v->next)
+    {
+        aup = v->data.ptrvalue;
+        if(aup->name->choice != 2)
+            continue;
+
+        namestd = aup->name->data;
+        for(i = 0; i < numnew; i++)
+        {
+            if(StringICmp(namestd->names[0], mu[i]) == 0)
+            {
+                match++;
+                break;
+            }
+        }
+    }
+
+    i = (num < numnew) ? num : numnew;
+    if(i > 3 * match)
+        return(FALSE);
+
+    if(num > 10 || numnew == 0)
+    {
+        AuthListFree(art_tmp->authors);
+        art_tmp->authors = art->authors;
+        art->authors = NULL;
+    }
+    return(TRUE);
 }
+
 /*****************************************************************************
 *
 *   FindPub
diff --git a/network/nsclilib/ni_debug.c b/network/nsclilib/ni_debug.c
index 5ecfbe8c..a344b73c 100644
--- a/network/nsclilib/ni_debug.c
+++ b/network/nsclilib/ni_debug.c
@@ -1,47 +1,50 @@
-/*  $RCSfile: ni_debug.c,v $  $Revision: 6.3 $  $Date: 2001/02/21 22:09:27 $
-* ==========================================================================
-*
-*                            PUBLIC DOMAIN NOTICE
-*               National Center for Biotechnology Information
-*
-*  This software/database is a "United States Government Work" under the
-*  terms of the United States Copyright Act.  It was written as part of
-*  the author's official duties as a United States Government employee and
-*  thus cannot be copyrighted.  This software/database is freely available
-*  to the public for use. The National Library of Medicine and the U.S.
-*  Government have not placed any restriction on its use or reproduction.
-*
-*  Although all reasonable efforts have been taken to ensure the accuracy
-*  and reliability of the software and data, the NLM and the U.S.
-*  Government do not and cannot warrant the performance or results that
-*  may be obtained by using this software or data. The NLM and the U.S.
-*  Government disclaim all warranties, express or implied, including
-*  warranties of performance, merchantability or fitness for any particular
-*  purpose.
-*
-*  Please cite the author in any work or product based on this material.
-*
-* ==========================================================================
-*
-* Author:  Denis Vakatov
-*
-* File Description:
-*   Basic client code for the debug NCBI client that connects
-*   directly to the standalone server(bypasses NCBI dispatchers)
-*
-* --------------------------------------------------------------------------
-* $Log: ni_debug.c,v $
-* Revision 6.3  2001/02/21 22:09:27  lavr
-* SERVICE connector included
-*
-* Revision 6.2  1999/03/11 15:20:22  vakatov
-* Added "timeout" arg to SOCK_Create() and SOCK_Reconnect()
-*
-* Revision 6.1  1998/05/05 22:23:35  vakatov
-* Initial revision
-*
-* ==========================================================================
-*/
+/* $Id: ni_debug.c,v 6.4 2003/10/27 14:11:10 lavr Exp $
+ * ==========================================================================
+ *
+ *                            PUBLIC DOMAIN NOTICE
+ *               National Center for Biotechnology Information
+ *
+ *  This software/database is a "United States Government Work" under the
+ *  terms of the United States Copyright Act.  It was written as part of
+ *  the author's official duties as a United States Government employee and
+ *  thus cannot be copyrighted.  This software/database is freely available
+ *  to the public for use. The National Library of Medicine and the U.S.
+ *  Government have not placed any restriction on its use or reproduction.
+ *
+ *  Although all reasonable efforts have been taken to ensure the accuracy
+ *  and reliability of the software and data, the NLM and the U.S.
+ *  Government do not and cannot warrant the performance or results that
+ *  may be obtained by using this software or data. The NLM and the U.S.
+ *  Government disclaim all warranties, express or implied, including
+ *  warranties of performance, merchantability or fitness for any particular
+ *  purpose.
+ *
+ *  Please cite the author in any work or product based on this material.
+ *
+ * ==========================================================================
+ *
+ * Author:  Denis Vakatov
+ *
+ * File Description:
+ *   Basic client code for the debug NCBI client that connects
+ *   directly to the standalone server (bypasses NCBI dispatchers)
+ *
+ * --------------------------------------------------------------------------
+ * $Log: ni_debug.c,v $
+ * Revision 6.4  2003/10/27 14:11:10  lavr
+ * Old (Shavirin's) dispatchers disabled unconditionally
+ *
+ * Revision 6.3  2001/02/21 22:09:27  lavr
+ * SERVICE connector added
+ *
+ * Revision 6.2  1999/03/11 15:20:22  vakatov
+ * Added "timeout" arg to SOCK_Create() and SOCK_Reconnect()
+ *
+ * Revision 6.1  1998/05/05 22:23:35  vakatov
+ * Initial revision
+ *
+ * ==========================================================================
+ */
 
 #include <ncbi.h>
 #include <ncbinet.h>
diff --git a/network/nsclilib/ni_defin.h b/network/nsclilib/ni_defin.h
index 2ece93ff..20e07519 100644
--- a/network/nsclilib/ni_defin.h
+++ b/network/nsclilib/ni_defin.h
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:        1/1/92
 *
-* $Revision: 6.2 $
+* $Revision: 6.3 $
 *
 * File Description:
 *
@@ -48,6 +48,9 @@
 *
 * RCS Modification History:
 * $Log: ni_defin.h,v $
+* Revision 6.3  2003/05/05 12:24:26  rsmith
+* range of socket errors is from WSABASEERR to WSABASEERR + 2000, not + sys_nerr. Allows cross compilation by Codewarrior.
+*
 * Revision 6.2  2001/05/08 16:43:57  juran
 * Use errno, not errno_long.
 *
@@ -241,7 +244,8 @@
 #define errno                                   WSAGetLastError()
 #define _INVALID_SOCKET_DEFINED_
 #define NI_BLOCK_WITH_FUNCTION
-#define SOCK_INDEX_ERRNO                        ((errno <= WSABASEERR || errno >= sys_nerr + WSABASEERR) ? 0 : (errno - WSABASEERR))
+/* see WinSock2.h and winerror.h for why 2000 */
+#define SOCK_INDEX_ERRNO                        ((errno <= WSABASEERR || errno >= 2000 + WSABASEERR) ? 0 : (errno - WSABASEERR))
 #endif /* NETP_INET_WINSOCK */
 
 /* TGV's Multinet TCP/IP suite for OpenVMS */
diff --git a/network/nsclilib/ni_disp.c b/network/nsclilib/ni_disp.c
index 73a1564c..4871a619 100644
--- a/network/nsclilib/ni_disp.c
+++ b/network/nsclilib/ni_disp.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:        1/1/92
 *
-* $Revision: 4.12 $
+* $Revision: 4.15 $
 *
 * File Description:
 *   This file is a library of functions to be used by server application
@@ -268,6 +268,15 @@
 *
 * RCS Modification History:
 * $Log: ni_disp.c,v $
+* Revision 4.15  2003/09/17 15:38:06  rsmith
+* include unistd.h for Windows (yes MS-Windows) when compiling with Codewarrior only.
+*
+* Revision 4.14  2003/09/17 13:38:48  ivanov
+* Include unistd.h only for OS_UNIX
+*
+* Revision 4.13  2003/09/15 18:45:55  rsmith
+* add unistd.h include for write and dup.
+*
 * Revision 4.12  2002/11/06 21:30:08  ucko
 * Don't assume MIPS is IRIX, or HPPA is HP/UX; allow Linux too, for both.
 *
@@ -384,6 +393,9 @@
 #include "ncbinet.h"
 #include "ni_lib.h"
 #include "ni_msg.h"
+#if defined(OS_MSWIN)  &&  defined(COMP_METRO)
+#  include <unistd.h> /* for write and dup with MW compiler. */
+#endif
 
 /* missing prototypes */
 #ifdef __cplusplus
@@ -689,11 +701,11 @@ NLM_EXTERN Int2 NI_InitServices(NI_DispatcherPtr disp, CharPtr user, CharPtr gro
 
         MemSet(&buffer, 0, sizeof(buffer));
 
-	if ((fp = popen("uname -a","r")) != NULL)
-	{
-	    FileRead (buffer, 1, sizeof (buffer), fp);
-	    stackDescription = StringSave(buffer);
-	    pclose(fp);
+        if ((fp = popen("uname -a","r")) != NULL)
+        {
+            FileRead (buffer, 1, sizeof (buffer), fp);
+            stackDescription = StringSave(buffer);
+            pclose(fp);
             for (status = StrLen(stackDescription) - 1; status >= 0; status--)
             {
                 /* convert characters which are incompatible with VisibleString */
@@ -2822,10 +2834,10 @@ NLM_EXTERN Int2 NI_GetPlatform (void)
 #endif
 #endif
 #ifdef OS_UNIX_NETBSD
-	retval = NI_PLATFORM_NETBSD;
+        retval = NI_PLATFORM_NETBSD;
 #endif
 #ifdef OS_UNIX_FREEBSD
-	retval = NI_PLATFORM_FREEBSD;
+        retval = NI_PLATFORM_FREEBSD;
 #endif
 #endif /* OS_UNIX */
 
@@ -3249,7 +3261,7 @@ static Int2 LIBCALLBACK NI_AsnWriteSTDOUT(Pointer p,CharPtr buf,Uint2 len)
 NLM_EXTERN NI_HandPtr NI_OpenASNIO(void)
 {
     NI_HandPtr  hp;
-    CharPtr	agent;
+    CharPtr     agent;
 
     if ((hp = MsgMakeHandle(FALSE)) == NULL)
         return NULL;
@@ -3263,7 +3275,7 @@ NLM_EXTERN NI_HandPtr NI_OpenASNIO(void)
 
     agent = getenv("HTTP_USER_AGENT");
     if(agent){
-	    hp->waip->writefunc=NI_AsnWriteSTDOUT;
+            hp->waip->writefunc=NI_AsnWriteSTDOUT;
     }
 
     LOG_SOCKET(hp->sok, TRUE);
diff --git a/network/nsclilib/ni_lib_.c b/network/nsclilib/ni_lib_.c
index 134cad32..4fdcede5 100644
--- a/network/nsclilib/ni_lib_.c
+++ b/network/nsclilib/ni_lib_.c
@@ -1,92 +1,108 @@
-/*  $RCSfile: ni_lib_.c,v $  $Revision: 4.10 $  $Date: 2002/04/16 21:34:20 $
-* ==========================================================================
-*
-*                            PUBLIC DOMAIN NOTICE
-*               National Center for Biotechnology Information
-*
-*  This software/database is a "United States Government Work" under the
-*  terms of the United States Copyright Act.  It was written as part of
-*  the author's official duties as a United States Government employee and
-*  thus cannot be copyrighted.  This software/database is freely available
-*  to the public for use. The National Library of Medicine and the U.S.
-*  Government have not placed any restriction on its use or reproduction.
-*
-*  Although all reasonable efforts have been taken to ensure the accuracy
-*  and reliability of the software and data, the NLM and the U.S.
-*  Government do not and cannot warrant the performance or results that
-*  may be obtained by using this software or data. The NLM and the U.S.
-*  Government disclaim all warranties, express or implied, including
-*  warranties of performance, merchantability or fitness for any particular
-*  purpose.
-*
-*  Please cite the author in any work or product based on this material.
-*
-* ==========================================================================
-*
-* Author:  Denis Vakatov
-*
-* File Description:
-*   Wraparound the old NCBI network client API.
-*   Now provides new mechanisms to connect clients to the NCBI network 
-*   services
-*
-* --------------------------------------------------------------------------
-* $Log: ni_lib_.c,v $
-* Revision 4.10  2002/04/16 21:34:20  lavr
-* Disable old dispatcher completely and unconditionally
-*
-* Revision 4.9  2001/02/21 22:09:27  lavr
-* SERVICE connector included
-*
-* Revision 4.8  1998/09/08 17:59:06  vakatov
-* Added WWW/Firewall network interface
-*
-* Revision 4.7  1998/05/05 22:45:37  vakatov
-* Added "eNII_Debug" network interface
-*
-* Revision 4.6  1998/04/15 20:01:20  vakatov
-* [OS_MAC, ALLOW_STATELESS]  Stateless mode now available on Mac
-*
-* Revision 4.5  1998/04/10 19:24:47  vakatov
-* NI_SetInterface():  return the overridden(old) interface value; check
-* for the validity of the new interface
-*
-* Revision 4.4  1998/04/03 22:54:46  vakatov
-* Support *stateless* WWW connection only if #ALLOW_STATELESS is defined
-* (thus, disable it by default)
-*
-* Revision 4.3  1998/03/31 00:27:04  kans
-* for Mac, define NI_WWW_SUPPORTED
-*
-* Revision 4.2  1998/03/30 17:50:17  vakatov
-* Ingrafted to the main NCBI CVS tree
-*
-* ==========================================================================
-*/
+/*  $RCSfile: ni_lib_.c,v $  $Revision: 4.12 $  $Date: 2003/10/27 14:11:10 $
+ * ==========================================================================
+ *
+ *                            PUBLIC DOMAIN NOTICE
+ *               National Center for Biotechnology Information
+ *
+ *  This software/database is a "United States Government Work" under the
+ *  terms of the United States Copyright Act.  It was written as part of
+ *  the author's official duties as a United States Government employee and
+ *  thus cannot be copyrighted.  This software/database is freely available
+ *  to the public for use. The National Library of Medicine and the U.S.
+ *  Government have not placed any restriction on its use or reproduction.
+ *
+ *  Although all reasonable efforts have been taken to ensure the accuracy
+ *  and reliability of the software and data, the NLM and the U.S.
+ *  Government do not and cannot warrant the performance or results that
+ *  may be obtained by using this software or data. The NLM and the U.S.
+ *  Government disclaim all warranties, express or implied, including
+ *  warranties of performance, merchantability or fitness for any particular
+ *  purpose.
+ *
+ *  Please cite the author in any work or product based on this material.
+ *
+ * ==========================================================================
+ *
+ * Author:  Denis Vakatov
+ *
+ * File Description:
+ *   Wraparound the old NCBI network client API.
+ *   Now provides new mechanisms to connect clients to the NCBI network 
+ *   services
+ *
+ * --------------------------------------------------------------------------
+ * $Log: ni_lib_.c,v $
+ * Revision 4.12  2003/10/27 14:11:10  lavr
+ * Old (Shavirin's) dispatchers disabled unconditionally
+ *
+ * Revision 4.11  2003/10/16 15:11:52  lavr
+ * SRV_CONN_MODE made case-insensitive
+ *
+ * Revision 4.10  2002/04/16 21:34:20  lavr
+ * Disable old dispatcher completely and unconditionally
+ *
+ * Revision 4.9  2001/02/21 22:09:27  lavr
+ * SERVICE connector added
+ *
+ * Revision 4.8  1998/09/08 17:59:06  vakatov
+ * Added WWW/Firewall network interface
+ *
+ * Revision 4.7  1998/05/05 22:45:37  vakatov
+ * Added "eNII_Debug" network interface
+ *
+ * Revision 4.6  1998/04/15 20:01:20  vakatov
+ * [OS_MAC, ALLOW_STATELESS]  Stateless mode now available on Mac
+ *
+ * Revision 4.5  1998/04/10 19:24:47  vakatov
+ * NI_SetInterface():  return the overridden(old) interface value; check
+ * for the validity of the new interface
+ *
+ * Revision 4.4  1998/04/03 22:54:46  vakatov
+ * Support *stateless* WWW connection only if #ALLOW_STATELESS is defined
+ * (thus, disable it by default)
+ *
+ * Revision 4.3  1998/03/31 00:27:04  kans
+ * for Mac, define NI_WWW_SUPPORTED
+ *
+ * Revision 4.2  1998/03/30 17:50:17  vakatov
+ * Ingrafted to the main NCBI CVS tree
+ *
+ * ==========================================================================
+ */
 
 #include <ncbinet.h>
 #include <ncbithr.h>
 
-/* From now on, the old-fashioned interface is NOT supported for all platforms
- */
-#undef NI_DISP_SUPPORTED
-
 /* WWW(HTTPD)-based interfaces are supported on selected platforms
  */
 #if defined(OS_UNIX) || defined(OS_MSWIN) || defined(OS_MAC)
-#define NI_WWW_SUPPORTED
-#define NI_WWWFIREWALL_SUPPORTED
-#ifdef ALLOW_STATELESS 
-#define NI_WWWDIRECT_SUPPORTED
-#endif
-#define NI_SERVICE_SUPPORTED
-#define NI_DEBUG_SUPPORTED
+#  define NI_WWW_SUPPORTED
+#  define NI_WWWFIREWALL_SUPPORTED
+#  ifdef ALLOW_STATELESS 
+#    define NI_WWWDIRECT_SUPPORTED
+#  endif
+#  define NI_SERVICE_SUPPORTED
+#  define NI_DEBUG_SUPPORTED
 #endif /* OS_UNIX | OS_MSWIN | OS_MAC */
 
+/* From now on the old-fashioned interfaces are NOT supported for all platforms
+ */
+#ifdef NI_DISP_SUPPORTED
+#  undef NI_DISP_SUPPORTED
+#endif
+#ifdef NI_WWW_SUPPORTED
+#  undef NI_WWW_SUPPORTED
+#endif
+#ifdef NI_WWWFIREWALL_SUPPORTED
+#  undef NI_WWWFIREWALL_SUPPORTED
+#endif
+#ifdef NI_WWWDIRECT_SUPPORTED
+#  undef NI_WWWDIRECT_SUPPORTED
+#endif
 
 /* Override config-file value by the environment variable's value, if any */
 #if defined(OS_UNIX) || defined(OS_MSWIN)
-#define USE_GETENV
+#  define USE_GETENV
 #endif /* OS_UNIX | OS_MSWIN */
 
 
@@ -184,17 +200,17 @@ static NIOptions* s_GetNIOptions
 
   NI_GetEnvParam(conf_file, conf_section, ENV_CONN_MODE,
                  conn_mode, sizeof(conn_mode), "");
-  if (StringCmp(conn_mode, DISPATCHER_MODE) == 0)
+  if (StringICmp(conn_mode, DISPATCHER_MODE) == 0)
     nio->interface = eNII_Dispatcher;
-  else if (StringCmp(conn_mode, WWW_CLIENT_MODE) == 0)
+  else if (StringICmp(conn_mode, WWW_CLIENT_MODE) == 0)
     nio->interface = eNII_WWW;
-  else if (StringCmp(conn_mode, WWW_FIREWALL_MODE) == 0)
+  else if (StringICmp(conn_mode, WWW_FIREWALL_MODE) == 0)
     nio->interface = eNII_WWWFirewall;
-  else if (StringCmp(conn_mode, WWW_DIRECT_MODE) == 0)
+  else if (StringICmp(conn_mode, WWW_DIRECT_MODE) == 0)
     nio->interface = eNII_WWWDirect;
-  else if (StringCmp(conn_mode, SERVICE_MODE) == 0)
+  else if (StringICmp(conn_mode, SERVICE_MODE) == 0)
     nio->interface = eNII_Service;
-  else if (StringCmp(conn_mode, DEBUG_MODE) == 0)
+  else if (StringICmp(conn_mode, DEBUG_MODE) == 0)
     nio->interface = eNII_Debug;
   else
     nio->interface = NII_DEFAULT;
diff --git a/network/nsclilib/ni_macdv.c b/network/nsclilib/ni_macdv.c
index 916b366a..2ad8a5e5 100644
--- a/network/nsclilib/ni_macdv.c
+++ b/network/nsclilib/ni_macdv.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:        1/13/95
 *
-* $Revision: 6.3 $
+* $Revision: 6.4 $
 *
 * File Description: 
 *   Determine which Macintosh MacTCP device is in-use (e.g., "Ethernet", "PPP")
@@ -51,6 +51,9 @@
 *
 * RCS Modification History:
 * $Log: ni_macdv.c,v $
+* Revision 6.4  2003/05/05 12:27:37  rsmith
+* add Mac OS guards so we can cross compile this project to Windows w/o changing files in the project.
+*
 * Revision 6.3  2001/04/20 18:31:58  juran
 * Bring obsolete preprocessor symbol up to date.
 *
@@ -86,6 +89,8 @@
  *
 */
 
+#if defined(OS_MAC)  ||  defined(OS_UNIX_DARWIN)
+ 
 #include <ncbi.h>
 #include <ncbiwin.h>
 
@@ -425,3 +430,5 @@ SearchFolderForRsrc( FSSpec *target, short vRefNum, long dirID,
     SetResLoad( oldResLoad );
     return err;
 }
+
+#endif  /* defined(OS_MAC)  ||  defined(OS_UNIX_DARWIN) */
diff --git a/network/nsclilib/ni_service.c b/network/nsclilib/ni_service.c
index 4c5d4d12..d56b8511 100644
--- a/network/nsclilib/ni_service.c
+++ b/network/nsclilib/ni_service.c
@@ -1,4 +1,4 @@
-/*  $RCSfile: ni_service.c,v $  $Revision: 6.13 $  $Date: 2002/11/26 17:00:11 $
+/*  $RCSfile: ni_service.c,v $  $Revision: 6.16 $  $Date: 2003/10/27 14:10:49 $
  * ==========================================================================
  *
  *                            PUBLIC DOMAIN NOTICE
@@ -30,6 +30,16 @@
  *
  * --------------------------------------------------------------------------
  * $Log: ni_service.c,v $
+ * Revision 6.16  2003/10/27 14:10:49  lavr
+ * Better flow control in s_AsnWrite()
+ *
+ * Revision 6.15  2003/10/16 15:12:38  lavr
+ * Better flow control in s_AsnWrite()
+ *
+ * Revision 6.14  2003/10/10 19:23:58  lavr
+ * Perform persistent ASN.1 write to connection in a tight loop
+ * (work around bug in AsnIoWriteBlock that otherwise generates err 79)
+ *
  * Revision 6.13  2002/11/26 17:00:11  lavr
  * Recognize "SOME" and "DATA" as keyword values of "SRV_DEBUG_PRINTOUT"
  *
@@ -104,18 +114,30 @@
 /* Static functions
  */
 
-static Int2 LIBCALLBACK s_AsnRead(Pointer p, CharPtr buff, Uint2 len)
+static Int2 LIBCALLBACK s_AsnRead(Pointer p, CharPtr buf, Uint2 len)
 {
-    size_t n_read = 0;
-    CONN_Read((CONN) p, buff, len, &n_read, eIO_ReadPlain);
+    size_t n_read;
+    CONN_Read((CONN) p, buf, len, &n_read, eIO_ReadPlain);
     return (Int2) n_read;
 }
 
 
-static Int2 LIBCALLBACK s_AsnWrite(Pointer p, CharPtr buff, Uint2 len)
+static Int2 LIBCALLBACK s_AsnWrite(Pointer p, CharPtr buf, Uint2 len)
 {
+    CONN   conn = (CONN) p;
     size_t n_written = 0;
-    CONN_Write((CONN) p, buff, len, &n_written);
+    for (;;) {
+        size_t     x_written;
+        EIO_Status status = CONN_Write(conn, buf, len, &x_written);
+        n_written += x_written;
+        if (len == x_written  ||  status != eIO_Success  ||
+            CONN_Wait(conn, eIO_Write,
+                      CONN_GetTimeout(conn, eIO_Write)) != eIO_Success) {
+            break;
+        }
+        buf += x_written;
+        len -= x_written;
+    }
     return (Int2) n_written;
 }
 
diff --git a/network/nsclilib/readme b/network/nsclilib/readme
index 15a8a0b0..c68748ad 100644
--- a/network/nsclilib/readme
+++ b/network/nsclilib/readme
@@ -83,13 +83,14 @@ Value:
 | Thus the mapping on your non-transparent firewall server
 | should look like this:
 | 
-| SRV_PROXY_HOST:5853       --> 130.14.22.1:5853  RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5859       --> 130.14.22.2:5859  RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5840       --> 130.14.22.8:5840  RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5810       --> 130.14.22.30:5810 RETIRED -- DO NOT USE!
-| SRV_PROXY_HOST:5812       --> 130.14.22.31:5812
-| SRV_PROXY_HOST:5811       --> 130.14.22.32:5811
-| SRV_PROXY_HOST:5850..5860 --> 130.14.29.112:5850..5860(for future extensions)
+| SRV_PROXY_HOST:5853       --> 130.14.22.1:5853  RETIRED  -- DO NOT USE!
+| SRV_PROXY_HOST:5859       --> 130.14.22.2:5859  RETIRED  -- DO NOT USE!
+| SRV_PROXY_HOST:5840       --> 130.14.22.8:5840  RETIRED  -- DO NOT USE!
+| SRV_PROXY_HOST:5810       --> 130.14.22.30:5810 RETIRED  -- DO NOT USE!
+| SRV_PROXY_HOST:5845       --> 130.14.22.12:5845 INTERNAL
+| SRV_PROXY_HOST:5812       --> 130.14.22.31:5812 OBSOLESCENT
+| SRV_PROXY_HOST:5811       --> 130.14.22.32:5811 OBSOLESCENT
+| SRV_PROXY_HOST:5850..5860 --> 130.14.29.112:5850..5860
 | 
 | NOTE:  It's pretty rare (if ever) when you have to use
 |        "SRV_PROXY_HOST" as most of firewalls are "transparent"
@@ -188,4 +189,4 @@ Solaris or IRIX. Then, the client must run on the host that:
 a) belongs to one of NCBI subnets and
 b) has "lbdaemon"(load-balance daemon) application running on it.
 
-$Date: 2003/02/08 17:51:14 $
+$Date: 2003/09/29 15:05:10 $
diff --git a/network/taxon1/common/taxon1.asn b/network/taxon1/common/taxon1.asn
index 2b1e3d62..7b28cb39 100644
--- a/network/taxon1/common/taxon1.asn
+++ b/network/taxon1/common/taxon1.asn
@@ -1,4 +1,4 @@
---$Revision: 6.5 $
+--$Revision: 6.6 $
 --**********************************************************************
 --
 --  NCBI Taxonomy Server
@@ -35,7 +35,10 @@ Taxon1-req ::= CHOICE {
 	id4gi		INTEGER,  	-- get taxid by gi
 	taxachildren	INTEGER,	-- get children
 	taxalineage     INTEGER,        -- get extended lineage for org
-	maxtaxid        NULL}           -- get max taxid
+        maxtaxid        NULL,           -- get max taxid
+        getproptypes    NULL,           -- get property types
+        getorgprop      Taxon1-info,    -- get properties for organism
+        searchname      Taxon1-info}    -- fancy search (token set, wild card)
 
 Taxon1-resp ::= CHOICE {
 	error		Taxon1-error,	-- sent on any error
@@ -59,7 +62,10 @@ Taxon1-resp ::= CHOICE {
 	taxabyid	Taxon2-data,
 	taxachildren	SEQUENCE OF Taxon1-name,
 	taxalineage	SEQUENCE OF Taxon1-name,
-	maxtaxid        INTEGER}
+        maxtaxid        INTEGER,
+	getproptypes    SET OF Taxon1-info,
+        getorgprop      SET OF Taxon1-info,
+        searchname      SET OF Taxon1-name}
 
 Taxon1-info ::= SEQUENCE {
 	ival1	INTEGER,
diff --git a/network/taxon1/taxon2/tc2proc.c b/network/taxon1/taxon2/tc2proc.c
index 7861336f..91632731 100644
--- a/network/taxon1/taxon2/tc2proc.c
+++ b/network/taxon1/taxon2/tc2proc.c
@@ -1,5 +1,5 @@
 /*----------------*/
-/* $Id: tc2proc.c,v 1.28 2003/03/05 21:32:00 soussov Exp $           */
+/* $Id: tc2proc.c,v 1.33 2003/07/29 20:06:05 soussov Exp $           */
 /*----------------*/
 
 #include <stdlib.h>
@@ -38,6 +38,7 @@ static Int2 GB_COMMON= 0;
 static Int2 GB_ACRONYM= 0;
 static Int2 GB_SYNONYM= 0;
 static Int2 GB_ANAMORPH= 0;
+static Int2 ANAMORPH= 0;
 
 static int my_timer= 0;
 
@@ -63,6 +64,7 @@ static Boolean we_want_synonyms= 0;
 static OrgRefPtr getFromBuff(Int4 id, int* is_sp, int* is_uncult, NameListPtr* bnl);
 static void loadInBuff(Int4 id);
 static void bldOrgRefOut(OrgRefPtr dst, OrgRefPtr src, Int4 tax_id);
+static int nof_tokens(char* s);
 
 Boolean tax1_setSynonyms(Boolean on_off)
 {
@@ -161,6 +163,7 @@ int InitTaxDB(void)
     GB_ACRONYM= tax_getClass_cde("genbank acronym");
     GB_SYNONYM= tax_getClass_cde("genbank synonym");
     GB_ANAMORPH= tax_getClass_cde("genbank anamorph");
+    ANAMORPH= tax_getClass_cde("anamorph");
 
     initBuff();
     tax_tree= tax_ptree_new();
@@ -778,12 +781,12 @@ static Int2 getSubtypeFromName(CharPtr name)
     c= StringStr(name, "subsp.");
     if(c == name) {
         rmWord(name, c, 6);
-        return 22;
+        return (nof_tokens(c) == 1)? 22 : 0;
     }
     c= StringStr(name, "ssp.");
     if(c == name) {
         rmWord(name, c, 4);
-        return 22;
+        return (nof_tokens(c) == 1)? 22 : 0;
     }
     c= StringStr(name, "f. sp.");
     if(c == name) {
@@ -882,9 +885,12 @@ static OrgModPtr bldOrgMod(TreeCursorPtr cursor)
 
     orgMdf->subtype= getSubtypeFromName(orgMdf->subname);
 
+    if(orgMdf->subtype == 22 && rank != SubspeciesRank + 1) 
+        orgMdf->subtype= 0;
+
     if(orgMdf->subtype <= 0) {
         if(--rank == SubspeciesRank) {
-            orgMdf->subtype= 22; /* subspecies */
+            if(nof_tokens(me->node_label) == 3) orgMdf->subtype= 22; /* subspecies */
         }
         else if(rank == tax_getRankId("varietas")) {
             orgMdf->subtype= 6; /* variety */
@@ -896,10 +902,15 @@ static OrgModPtr bldOrgMod(TreeCursorPtr cursor)
             orgMdf->subtype= 2; /* strain */
         }
         else {
-            orgMdf->subtype= 255; /* other */
+            orgMdf->subtype= 0; /* other */
         }
     }
     orgMdf->attrib= NULL;
+
+    if(orgMdf->subtype == 0) {
+        OrgModFree(orgMdf);
+        orgMdf= 0;
+    }
     
     return orgMdf;
 }
@@ -1541,8 +1552,9 @@ static int subtypeConflict(Int2 t1, Int2 t2)
     switch(t2) {
     case 2:
     case 6:
-    case 22:
-        if((t1 >= 2 && t1 <= 17) || (t1 == 22)) return 1;
+    /*case 22:*/
+/*        if((t1 >= 2 && t1 <= 17) || (t1 == 22)) return 1;*/
+        if((t1 >= 2 && t1 <= 17)) return 1;
         break;
     case 255:
         return 1;
@@ -2206,3 +2218,59 @@ Boolean tax1_inited()
 {
     return (tax_tree != NULL)? TRUE : FALSE;
 }
+
+static char* next_token(char* s)
+{
+    if(s == NULL) return NULL;
+
+    while(*s && (isspace(*s) || iscntrl(*s))) {
+        ++s;
+    }
+    
+    if(*s == '\0') return NULL;
+    else {
+        char last;
+        char first= *s;
+        int j= 0;
+
+        switch(first) {
+        case '"': last= '"'; break;
+        case '(': last= ')'; break;
+        case '{': last= '}'; break;
+        case '[': last= ']'; break;
+        default:  last= '\0';
+        }
+
+        for(++s; *s != '\0'; s++) {
+            if(!isalnum(*s)) {
+                if(last) {
+                    if(first == *s && first != '"') ++j;
+                    if(last == *s && (!j--)) {
+                        ++s;
+                        break;
+                    }
+                }
+                else {
+                    if(*s == '.' || isspace(*s) || iscntrl(*s)) {
+                        ++s;
+                        break;
+                    }
+                }
+            }
+        }
+            
+    }
+
+    return s;
+}
+
+
+static int nof_tokens(char* s)
+{
+    int n;
+    char* nt= s;
+
+    for(n= 0; (nt= next_token(nt)) != NULL; n++);
+
+    return n;
+}
diff --git a/network/taxon1/taxon2/txcdproc.c b/network/taxon1/taxon2/txcdproc.c
index ca27b0bb..2aab690f 100644
--- a/network/taxon1/taxon2/txcdproc.c
+++ b/network/taxon1/taxon2/txcdproc.c
@@ -29,7 +29,7 @@
 *
 * Version Creation Date:   07/15/97
 *
-* $Revision: 1.14 $
+* $Revision: 1.15 $
 *
 * File Description: 
 *       API for Taxonomy service
@@ -44,6 +44,9 @@
 *
 * RCS Modification History:
 * $Log: txcdproc.c,v $
+* Revision 1.15  2003/06/12 16:46:25  soussov
+* changes severity for AsnRead failures
+*
 * Revision 1.14  2003/03/06 16:30:32  kans
 * tdp->org needed a cast to (OrgRefPtr) due to Mac compiler complaint
 *
@@ -133,7 +136,7 @@ static clock_t tax_time1;
 static void report_service_error(CharPtr proc_name, Taxon1RespPtr taxbp)
 {
     if(taxbp == NULL) {
-	ErrPostEx(SEV_ERROR, 0, 0, "%s got NULL responce from service");
+	ErrPostEx(SEV_ERROR, 0, 0, "%s got NULL responce from service", proc_name);
     }
     else if(taxbp->choice == Taxon1Resp_error) {
 	Taxon1ErrorPtr tep= taxbp->data.ptrvalue;
@@ -163,7 +166,7 @@ static Taxon1RespPtr NetTaxArchReadAsn(void)
 
     if ((taxbp == NULL) || ErrFetch(&err))
     {
-        ErrPost (CTX_UNKNOWN, 1, "Null message read from server");
+        ErrPostEx (SEV_WARNING, 1, 1, "Null message read from server");
     }
     ErrSetOpts(erract, 0);
 
@@ -1201,7 +1204,7 @@ static Boolean GenericReestablishNet(CharPtr svcName, Boolean showErrs)
 	    retval = myNetInit();
 	}
         else {
-            ErrPost(CTX_UNKNOWN, 1, "Unable to re-contact dispatcher");
+            ErrPostEx(SEV_ERROR, 1,2, "Unable to re-contact dispatcher");
             if (showErrs) {
                 ErrShow();
             }
@@ -1212,8 +1215,8 @@ static Boolean GenericReestablishNet(CharPtr svcName, Boolean showErrs)
 
     if (! retval )
     {
-        sprintf (buf, "Unable to re-establish %s service", svcName);
-        ErrPost(CTX_UNKNOWN, 1, buf);
+        /*sprintf (buf, "Unable to re-establish %s service", svcName);*/
+        ErrPostEx(SEV_ERROR, 1, 3, "Unable to re-establish %s service", svcName);
         if (showErrs) {
             ErrShow();
         }
diff --git a/network/vibnet/netcnfg.c b/network/vibnet/netcnfg.c
index d7bb3706..91cc1e47 100644
--- a/network/vibnet/netcnfg.c
+++ b/network/vibnet/netcnfg.c
@@ -23,7 +23,7 @@
  *
  * ===========================================================================
  *
- * RCS $Id: netcnfg.c,v 6.14 1999/08/31 22:25:23 kans Exp $
+ * RCS $Id: netcnfg.c,v 6.15 2003/09/11 05:28:02 kans Exp $
  *
  * Author:  Kans, Epstein
  *
@@ -148,7 +148,8 @@ static void AcceptNetConfigForm (ButtoN b)
     Update ();
     return;
   } else if (val == 3) {
-    SetAppParam ("NCBI", "NET_SERV", "SRV_CONN_MODE", "FIREWALL");
+    SetAppParam ("NCBI", "NET_SERV", "SRV_CONN_MODE", "SERVICE");
+    SetAppParam ("NCBI", "NET_SERV", "FIREWALL", "TRUE");
     GetTitle (ncp->proxyHost, str, sizeof (str));
     if (! StringHasNoText (str)) {
       SetAppParam ("NCBI", "NET_SERV", "SRV_HTTP_PROXY_HOST", str);
@@ -173,6 +174,7 @@ static void AcceptNetConfigForm (ButtoN b)
     }
   } else {
     SetAppParam ("NCBI", "NET_SERV", "SRV_CONN_MODE", NULL);
+    SetAppParam ("NCBI", "NET_SERV", "FIREWALL", NULL);
     SetAppParam ("NCBI", "NET_SERV", "SRV_HTTP_PROXY_HOST", NULL);
     SetAppParam ("NCBI", "NET_SERV", "SRV_HTTP_PROXY_PORT", NULL);
     SetAppParam ("NCBI", "NET_SERV", "SRV_PROXY_HOST", NULL);
@@ -212,6 +214,7 @@ static void AcceptNetConfigForm (ButtoN b)
   }
 
   if (NoEntryExists ("SRV_CONN_MODE") &&
+      NoEntryExists ("FIREWALL") &&
       NoEntryExists ("SRV_CONN_TIMEOUT") &&
       NoEntryExists ("SRV_ENGINE_HOST") &&
       NoEntryExists ("SRV_ENGINE_PORT") &&
@@ -420,6 +423,12 @@ extern void ShowNetConfigForm (WndActnProc activate, FormMessageFunc messages,
     } else if (GetAppParam ("NCBI", "NET_SERV", "SRV_CONN_MODE", "WWW", str, sizeof (str))) {
       if (StringICmp (str, "FIREWALL") == 0) {
         SafeSetValue (ncp->srvConnMode, 3);
+      } else if (StringICmp (str, "SERVICE") == 0) {
+        if (GetAppParam ("NCBI", "NET_SERV", "FIREWALL", "WWW", str, sizeof (str))) {
+          if (StringICmp (str, "TRUE") == 0) {
+            SafeSetValue (ncp->srvConnMode, 3);
+          }
+        }
       }
     }
     if (GetAppParam ("NCBI", "NET_SERV", "SRV_HTTP_PROXY_HOST", NULL, str, sizeof (str))) {
diff --git a/network/wwwblast/.WWWBLAST_VERSION b/network/wwwblast/.WWWBLAST_VERSION
new file mode 100644
index 00000000..bda8fbec
--- /dev/null
+++ b/network/wwwblast/.WWWBLAST_VERSION
@@ -0,0 +1 @@
+2.2.6
diff --git a/network/wwwblast/README.rps b/network/wwwblast/README.rps
new file mode 100644
index 00000000..d057e9d8
--- /dev/null
+++ b/network/wwwblast/README.rps
@@ -0,0 +1,201 @@
+RPS Blast: Reversed Position Specific Blast
+
+
+RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database 
+of profiles.  This is the opposite of PSI-BLAST that searches a profile 
+against a database of sequences, hence the 'Reverse'.  RPS-BLAST
+uses a BLAST-like algorithm, finding single- or double-word hits
+and then performing an ungapped extension on these candidate matches.
+If a sufficiently high-scoring ungapped alignment is produced, a gapped
+extension is performed and those (gapped) alignments with sufficiently
+low expect value are reported.  This procedure is in contrast to IMPALA
+that performs a Smith-Waterman calculation between the query and 
+each profile, rather than using a word-hit approach to identify
+matches that should be extended.
+
+RPS-BLAST uses a BLAST database, with addition of some other files that
+contain a precomputed lookup table for the profiles to allow the search
+to proceed faster.  Unfortunately it was not possible to make this
+lookup table architecture independent (like the BLAST databases themselves)
+and one cannot take an RPS-BLAST database prepared on a big-endian
+system (e.g., Solaris Sparc) and run it on a small-endian system
+(e.g., NT).  The RPS-BLAST database must be prepared again for the small-endian
+system.
+
+The CD-Search databases for RPS-BLAST can be found at:
+
+ ftp://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/
+
+It is necessary to untar the archive and run copymat and formatdb. 
+It is not necessary to run makemat on the databases from this
+directory.
+
+RPS-BLAST was coded by Sergei Shavirin with some help from Tom Madden.
+RPS-BLAST reuses some of the IMPALA code for precomputing the lookup tables 
+and all of the IMPALA code for evaluating the statistical significance of a match.  
+
+
+1. Binary files used in RPS Blast:
+
+The following binary files are used to setup and run RPS Blast:
+
+makemat	: primary profile preprocessor 
+  (converts a collection of binary profiles, created by the -C option
+   of PSI-BLAST, into portable ASCII form);
+
+copymat	: secondary profile preprocessor 
+  (converts ASCII matrices, produced by the primary preprocessor, 
+   into database that can be read into memory quickly);
+
+formatdb  : general BLAST database formatter.    
+
+rpsblast  : search program (searches a database of score 
+  matrices, prepared by copymat, producing BLAST-like output).
+
+2. Conversion of profiles into searchable database
+
+*Note*: if you are starting with *.mtx files obtained from the NCBI FTP site or
+another source you should skip the steps listed in 2.1.
+
+2.1. Primary preprocessing
+
+Prepare the following files:
+
+i.	a collection of PSI-BLAST-generated profiles with arbitrary 
+       names and suffix .chk; 
+
+ii.	a collection of "profile master sequences", associated with 
+    the profiles, each in a separate file with arbitrary name and a 3 character
+    suffix starting with c;
+    the sequences can have deflines; they need not be sequences in nr or
+    in any other sequence database; if the sequences have deflines, then
+    the deflines must be unique.
+
+iii.	a list of profile file names, one per line, named 
+    <database_name>.pn;
+
+iv.	a list of master sequence file names, one per line, in the same 
+    order as a list of profile names, named 
+     <database_name>.sn;
+
+The following files will be created:
+
+a.	a collection of ASCII files, corresponding to each of the 
+      original profiles, named 
+     <profile_name>.mtx;
+
+b.	a list of ASCII matrix files, named 
+      <database_name>.mn;
+
+c.	ASCII file with auxiliary information, named 
+       <database_name>.aux;
+
+Arguments to makemat:
+
+    -P database name (required)
+    -G Cost to open a gap (optional)
+       default = 11
+    -E Cost to extend a gap (optional)
+       default = 1
+    -U Underlying amino acid scoring matrix (optional)
+       default = BLOSUM62
+    -d Underlying sequence database used to create profiles (optional)
+       default = nr
+    -z Effective size of sequence database given by -d
+       default = current size of -d option
+       Note: It may make sense to use -z without -d when the
+       profiles were created with an older, smaller version of an
+       existing database 
+    -S  Scaling factor for  matrix outputs to avoid round-off problems
+       default = PRO_DEFAULT_SCALING_UP (currently defined as 100)
+       Use 1.0 to have no scaling
+       Output scores will be scaled back down to a unit scale to make
+       them look more like BLAST scores, but we found working with a larger
+       scale to help with roundoff problems.
+    -H get help (overrides all other arguments)
+Note: It is not enforced that the values of -G and -E passed to makemat
+were actually used in making the checkpoints. However, the values fed
+in to makemat are propagated to copymat and rpsblast.
+
+ATTENTION: It is strongly recommended to use -S 1 - the scaling factor
+	    should be set to 1 for rpsblast at this point in time.
+
+2.2. Secondary preprocessing
+
+Prepare the following files:
+
+i.	a collection of ASCII files, corresponding to each of the 
+  original profiles, named 
+  <profile_name>.mtx 
+(created by makemat);
+
+ii.	a collection of "profile master sequences", associated with 
+  the profiles, each in a separate file with arbitrary name and a 3 character
+  suffix starting with c.
+
+iii.	a list of ASCII_matrix files, named 
+     <database_name>.mn 
+   (created by makemat);
+
+iv.	a list of master sequence file names, one per
+  line, in the same order as a list of matrix names, named 
+  <database_name>.sn;
+
+v.	ASCII file with auxiliary information, named 
+  <database_name>.aux 
+(created by makemat);
+
+The files input to copymatices are in ASCII format and thus portable 
+between machines with different encodings for machine-readable files
+
+The following files will be created:
+
+a.	a huge binary file, containing all profile matrices, named
+ <database_name>.rps;
+b.     a huge binary file, containing lookup table for the Blast search
+ corresponding to matrixes named <database_name>.loo
+c.    File containing concatenation of all FASTA  "profile master sequences".
+     named  <database_name> (without extention)
+
+Arguments to copymat
+
+    -P database name (required)
+    -H get help (overrides all other arguments)
+    -r format data for RPS Blast
+
+ATTENTION: "-r" parameter have to be set to TRUE to format data for
+           RPS Blast at this step.
+
+NOTE: copymat requires a fair amount of memory as it first constructs
+the the lookup table in memory before writing it to disk.  Users have
+found that they require a machine with at least 500 Meg of memory for this
+task.
+
+2.3 Creating of BLAST database from <database_name> file containing
+    all "profile master sequences".
+
+"formatdb" program should be run to create regular BLAST database of all
+"profile master sequences":
+
+    formatdb -i <database_name>    -o T
+
+3. Search
+
+Arguments to RPS Blast
+
+   -i  query sequence file (required)
+   -p  if query sequence protein (if FALSE 6 frame franslation will be
+                                  conducted as in blastx program)
+   -P  database of profiles (required)
+   -o  output file (optional)
+       default = stdout
+   -e  Expectation value threshold  (E), (optional, same as for BLAST)
+       default = 10 
+   -m  alignment view (optional, same as for BLAST)
+   -z  effective length of database (optional)
+       -1 = length given via -z option to makemat
+       default (0) implies  length is actual length of profile library
+          adjusted for end effects
+
+
+
diff --git a/network/wwwblast/Src/Makefile b/network/wwwblast/Src/Makefile
new file mode 100644
index 00000000..8ea0c4c3
--- /dev/null
+++ b/network/wwwblast/Src/Makefile
@@ -0,0 +1,114 @@
+# Set the NCBI variable to your local path to the NCBI toolkit!
+#NCBI = 
+
+NCBI_INCDIR = $(NCBI)/include
+NCBI_ALTLIB = $(NCBI)/altlib
+NCBI_LIBDIR = $(NCBI)/lib
+
+NCBI_OTHERLIBS = -lm
+THREAD_LIBS = -lpthread
+
+# Uncomment the line(s) relevant to your platform below:
+
+# Solaris Intel 
+#NCBI_OTHERLIBS += -lposix4 -lresolv -lsocket -lrpcsvc -lnsl -lgen
+# Solaris Sparc
+#NCBI_OTHERLIBS += -lposix4 -lresolv -lsocket -lrpcsvc -lnsl
+# Darwin
+#NCBI_OTHERLIBS = -lc
+#THREAD_LIBS =
+#DEFINE = -DDARWIN
+
+#
+CC=cc 
+
+BLAST_LIBS = -lncbitool -lncbiobj -lncbi $(NCBI_OTHERLIBS)
+# For standalone model
+ALL_LIBS = -lncbidesk -lvibgif $(BLAST_LIBS) $(THREAD_LIBS)
+# For NCBI Client-server model
+ALL_LIBS_CS = -lncbitxc2 -lncbiid1 -lnetblast -lnetcli $(ALL_LIBS)
+BL2_LIBS = $(BLAST_LIBS)
+# For Blast 2 sequences client/server
+BL2_LIBS_CS = -lncbiid1 -lnetcli $(BLAST_LIBS)
+
+BL2_DEFINE = -DBL2SEQ_STANDALONE
+
+# For NCBI compilation with signal handling
+# The following 2 lines are for internal NCBI BLAST 2 sequences only.
+# Comment out for standalone.
+#BL2_OBJ = qblastnet.o objBlobj.o $(LIBS)/ncbithr.o
+#BL2_LIBS_CS = -lncbiid1 -lnetblast -lnetcli $(BLAST_LIBS) $(THREAD_LIBS)
+
+#DEBUG compilation
+LIBS = $(NCBI_ALTLIB)
+DEBUG_FLAG = -g
+
+#OPTIMIZED compilation
+LIBS = $(NCBI_LIBDIR)
+DEBUG_FLAG = -O
+
+OBJ_FILES = wwwbutl.c $(LIBS)/ncbithr.o
+
+#  Defines: 
+#  NCBI_CLIENT_SERVER - full NCBI Client/server including BLAST search
+#  NCBI_ENTREZ_CLIENT - Client server for gi/accession lookups
+
+INCDIR = -I. -I$(NCBI_INCDIR)
+
+# Additional include path for internal NCBI BLAST 2 sequences only.
+# Comment out for standalone
+#BLASTQUE = /home/dondosha/BlastQueue
+#INCDIR = -I$(BLASTQUE)/Client -I$(BLASTQUE)/ASN.1 -I. -I$(NCBI_INCDIR)
+
+# For standalone model
+CFLAGS=  $(DEBUG_FLAG) $(INCDIR)
+
+# Use client/server for gi/accession lookups
+CFLAGS_CS = $(DEBUG_FLAG) $(INCDIR) -DNCBI_ENTREZ_CLIENT
+
+# For full NCBI Client-server model
+#CFLAGS_FCS= -c $(DEBUG_FLAG) $(INCDIR) -DNCBI_CLIENT_SERVER
+
+.c.o:   Makefile
+	$(CC) -c $(CFLAGS) $<
+
+all: psiblast.REAL psiblast_cs.REAL  blast.REAL blast_cs.REAL nph-viewgif.cgi wblast2.REAL wblast2_cs.REAL bl2bag.cgi 
+
+blast.REAL: wwwblast.c $(OBJ_FILES) Makefile
+	$(CC)  $(CFLAGS) wwwblast.c $(OBJ_FILES) \
+	-L$(LIBS) $(ALL_LIBS) -o ./blast.REAL
+	mv ./blast.REAL ..
+blast_cs.REAL: wwwblast.c $(OBJ_FILES) Makefile
+	$(CC) $(CFLAGS_CS) wwwblast.c $(OBJ_FILES) \
+	-L$(LIBS) $(ALL_LIBS_CS) -o ./blast_cs.REAL
+	mv ./blast_cs.REAL ..
+psiblast.REAL: psiblast.o $(OBJ_FILES) Makefile
+	$(CC) $(CFLAGS) psiblast.o $(OBJ_FILES) \
+	-L$(LIBS) $(ALL_LIBS) -o ./psiblast.REAL
+	mv ./psiblast.REAL ../psiblast.REAL
+psiblast_cs.REAL: psiblast.o $(OBJ_FILES) Makefile
+	$(CC) $(CFLAGS_CS) psiblast.o $(OBJ_FILES) \
+	-L$(LIBS) $(ALL_LIBS_CS) -o ./psiblast_cs.REAL
+	mv ./psiblast_cs.REAL ../psiblast_cs.REAL
+nph-viewgif.cgi: viewgif.o
+	$(CC) viewgif.o -o nph-viewgif.cgi
+	mv nph-viewgif.cgi ..
+wblast2.REAL : wblast2.c 
+	$(CC) $(CFLAGS) $(BL2_DEFINE) wblast2.c \
+	-L$(LIBS) $(BL2_LIBS) -o ./wblast2.REAL
+	mv wblast2.REAL ..
+wblast2_cs.REAL : wblast2.c $(BL2_OBJ)
+	$(CC) $(CFLAGS_CS) $(BL2_DEFINE) wblast2.c $(BL2_OBJ) \
+	-L$(LIBS) $(BL2_LIBS_CS) -o ./wblast2_cs.REAL
+	mv wblast2_cs.REAL ..
+bl2bag.cgi : bl2bag.o
+	$(CC) bl2bag.o -L$(LIBS) -lncbi -lm -o bl2bag.cgi
+	mv bl2bag.cgi ..
+
+xml:
+	cd XML && make
+
+clean: 
+	rm *.o
+
+
diff --git a/network/wwwblast/Src/XML/Makefile b/network/wwwblast/Src/XML/Makefile
new file mode 100644
index 00000000..8e2d221c
--- /dev/null
+++ b/network/wwwblast/Src/XML/Makefile
@@ -0,0 +1,32 @@
+include $(NCBI)/ncbi.mk
+
+CC = $(NCBI_CC) 
+OTHERLIBS = $(NCBI_OTHERLIBS)
+#OTHERLIBS = $(NCBI_OTHERLIBS_MT)
+LIBPATH = $(NCBI_ALTLIB)
+#LIBPATH = $(NCBI_LIBDIR)
+OPTFLAGS = -g
+#OPTFLAGS = $(NCBI_OPTFLAG)
+INCPATH = $(NCBI_INCDIR)
+ASNTOOL=$(NCBI)/bin/asntool
+NCBI_ASNALL=/am/ncbiapdata/asn/asn.all
+
+all: bxmlobj.c
+
+# The present directory is included first to allow the Makefile to find
+# the local netblap1.h
+CFLAGS = $(CFLAGS1) $(OPTFLAGS) -I./ -I$(INCPATH) $(VIBFLAG) $(NEWASN2FF) -g 
+LDFLAGS = -I./ -I$(INCPATH) $(OPTFLAGS) -L$(LIBPATH) $(VIBFLAG) $(NEWASN2FF) -g 
+
+#bxmlobj.o: bxmlobj.c
+#	$(NCBI_CC) $(NCBI_CFLAGS1) $(OPTFLAGS) -I. -I$(NCBI_INCDIR) bxmlobj.c
+
+bxmlobj.c: $(NCBI_ASNALL) blstxml.asn
+	$(ASNTOOL) -m blstxml.asn -M $(NCBI_ASNALL) -B bxmlobj -G -w100 -Z
+	$(ASNTOOL) -m blstxml.asn -o blstxml.h -w 100 -Z
+	$(ASNTOOL) -m blstxml.asn -X NCBI_BlastOutput.mod
+#	mv bxmlobj.c ..
+#	mv blstxml.h ..
+#	mv bxmlobj.h ..
+clean:
+	rm -f *.h *.o *~ *.c
diff --git a/network/wwwblast/Src/XML/NCBI_BlastOutput.dtd b/network/wwwblast/Src/XML/NCBI_BlastOutput.dtd
new file mode 100644
index 00000000..1c9c5c2c
--- /dev/null
+++ b/network/wwwblast/Src/XML/NCBI_BlastOutput.dtd
@@ -0,0 +1,10 @@
+<!-- NCBI_BlastOutput.dtd
+  This file is built from a series of basic modules.
+  The actual ELEMENT and ENTITY declarations are in the modules.
+  This file is used to put them together.
+-->
+<!ENTITY % NCBI_Entity_module PUBLIC "-//NCBI//NCBI_Entity.mod//EN" "NCBI_Entity.mod">
+%NCBI_Entity_module;
+
+<!ENTITY % NCBI_BlastOutput_module PUBLIC "-//NCBI//NCBI_BlastOutput.mod//EN" "NCBI_BlastOutput.mod">
+%NCBI_BlastOutput_module;
diff --git a/network/wwwblast/Src/XML/NCBI_BlastOutput.mod b/network/wwwblast/Src/XML/NCBI_BlastOutput.mod
new file mode 100644
index 00000000..a628652c
--- /dev/null
+++ b/network/wwwblast/Src/XML/NCBI_BlastOutput.mod
@@ -0,0 +1,454 @@
+<!-- ============================================ -->
+<!-- This section mapped from ASN.1 module NCBI-BlastOutput -->
+ 
+<!-- ============================================ -->
+<!-- Definition of BlastOutput -->
+ 
+ 
+<!--
+$Id: NCBI_BlastOutput.mod,v 1.2 2003/04/21 18:42:44 dondosha Exp $
+ 
+$Revision: 1.2 $
+**********************************************************************
+ 
+  ASN.1 for simplified BLAST output in XML
+  by James Ostell, Yuri Wolf and Sergey Shavirin, 2000
+ 
+ 
+ $Log: NCBI_BlastOutput.mod,v $
+ Revision 1.2  2003/04/21 18:42:44  dondosha
+ Update of the module automatically generated from blstxml.asn
+
+ Revision 1.1  2002/12/02 19:43:46  dondosha
+ Copy of the namesake file in distrib/tools CVS directory
+ 
+ Revision 1.1  2002/12/02 19:42:22  dondosha
+ Copy of the namesake file in distrib/tools CVS directory
+ 
+ Revision 6.7  2002/07/17 22:28:13  dondosha
+ Added support for megablast XML output
+ 
+ Revision 6.6  2001/05/03 17:52:16  shavirin
+ Adopted for usage with mani-iterational XML definition.
+ 
+ Revision 6.4  2000/11/08 20:07:20  shavirin
+ Added new parameter align_len analogos to the number reported in
+ the Traditional Blast Output.
+ 
+ Revision 6.3  2000/10/23 20:24:03  shavirin
+ Few parameters were changed to OPTIONAL to allow XML without results:
+ failure or no hits found condition.
+ 
+ Revision 6.2  2000/08/11 17:48:35  shavirin
+ Small fix.
+ 
+ Revision 6.1  2000/08/09 20:43:12  shavirin
+ Initial revision.
+ 
+ 
+**********************************************************************
+ -->
+<!ELEMENT BlastOutput ( 
+               BlastOutput_program ,
+               BlastOutput_version ,
+               BlastOutput_reference ,
+               BlastOutput_db ,
+               BlastOutput_query-ID ,
+               BlastOutput_query-def ,
+               BlastOutput_query-len ,
+               BlastOutput_query-seq? ,
+               BlastOutput_param ,
+               BlastOutput_iterations ,
+               BlastOutput_mbstat? )>
+ 
+ 
+<!-- 
+ BLAST program: blastp, tblastx etc.
+ -->
+<!ELEMENT BlastOutput_program ( #PCDATA )>
+ 
+<!-- 
+ Program version 
+ -->
+<!ELEMENT BlastOutput_version ( #PCDATA )>
+ 
+<!-- 
+ Steven, David, Tom and others
+ -->
+<!ELEMENT BlastOutput_reference ( #PCDATA )>
+ 
+<!-- 
+ BLAST Database name
+ -->
+<!ELEMENT BlastOutput_db ( #PCDATA )>
+ 
+<!-- 
+ SeqId of query
+ -->
+<!ELEMENT BlastOutput_query-ID ( #PCDATA )>
+ 
+<!-- 
+ Definition line of query
+ -->
+<!ELEMENT BlastOutput_query-def ( #PCDATA )>
+ 
+<!-- 
+ length of query sequence
+ -->
+<!ELEMENT BlastOutput_query-len ( %INTEGER; )>
+ 
+<!-- 
+ query sequence itself
+ -->
+<!ELEMENT BlastOutput_query-seq ( #PCDATA )>
+ 
+<!-- 
+ search parameters
+ -->
+<!ELEMENT BlastOutput_param ( Parameters )>
+<!ELEMENT BlastOutput_iterations ( Iteration+ )>
+ 
+<!-- 
+ Mega BLAST search statistics
+ -->
+<!ELEMENT BlastOutput_mbstat ( Statistics )>
+ 
+ 
+ 
+ 
+ 
+<!-- Definition of Iteration -->
+ 
+<!ELEMENT Iteration ( 
+               Iteration_iter-num ,
+               Iteration_query-ID? ,
+               Iteration_query-def? ,
+               Iteration_query-len? ,
+               Iteration_hits? ,
+               Iteration_stat? ,
+               Iteration_message? )>
+ 
+ 
+<!-- 
+ iteration number
+ -->
+<!ELEMENT Iteration_iter-num ( %INTEGER; )>
+ 
+<!-- 
+ SeqId of query
+ -->
+<!ELEMENT Iteration_query-ID ( #PCDATA )>
+ 
+<!-- 
+ Definition line of query
+ -->
+<!ELEMENT Iteration_query-def ( #PCDATA )>
+ 
+<!-- 
+ length of query sequence
+ -->
+<!ELEMENT Iteration_query-len ( %INTEGER; )>
+ 
+<!-- 
+ Hits one for every db sequence
+ -->
+<!ELEMENT Iteration_hits ( Hit* )>
+ 
+<!-- 
+ search statistics            
+ -->
+<!ELEMENT Iteration_stat ( Statistics )>
+ 
+<!-- 
+ Some (error?) information
+ -->
+<!ELEMENT Iteration_message ( #PCDATA )>
+ 
+ 
+ 
+ 
+<!-- Definition of Parameters -->
+ 
+<!ELEMENT Parameters ( 
+               Parameters_matrix? ,
+               Parameters_expect ,
+               Parameters_include? ,
+               Parameters_sc-match? ,
+               Parameters_sc-mismatch? ,
+               Parameters_gap-open ,
+               Parameters_gap-extend ,
+               Parameters_filter? ,
+               Parameters_pattern? ,
+               Parameters_entrez-query? )>
+ 
+ 
+<!-- 
+ Matrix used (-M)
+ -->
+<!ELEMENT Parameters_matrix ( #PCDATA )>
+ 
+<!-- 
+ Expectation threshold (-e)
+ -->
+<!ELEMENT Parameters_expect ( %REAL; )>
+ 
+<!-- 
+ Inclusion threshold (-h)
+ -->
+<!ELEMENT Parameters_include ( %REAL; )>
+ 
+<!-- 
+ match score for NT (-r)
+ -->
+<!ELEMENT Parameters_sc-match ( %INTEGER; )>
+ 
+<!-- 
+ mismatch score for NT (-q)
+ -->
+<!ELEMENT Parameters_sc-mismatch ( %INTEGER; )>
+ 
+<!-- 
+ Gap opening cost (-G)
+ -->
+<!ELEMENT Parameters_gap-open ( %INTEGER; )>
+ 
+<!-- 
+ Gap extension cost (-E)
+ -->
+<!ELEMENT Parameters_gap-extend ( %INTEGER; )>
+ 
+<!-- 
+ Filtering options (-F)
+ -->
+<!ELEMENT Parameters_filter ( #PCDATA )>
+ 
+<!-- 
+ PHI-BLAST pattern
+ -->
+<!ELEMENT Parameters_pattern ( #PCDATA )>
+ 
+<!-- 
+ Limit of request to Entrez query
+ -->
+<!ELEMENT Parameters_entrez-query ( #PCDATA )>
+ 
+ 
+<!-- Definition of Statistics -->
+ 
+<!ELEMENT Statistics ( 
+               Statistics_db-num ,
+               Statistics_db-len ,
+               Statistics_hsp-len ,
+               Statistics_eff-space ,
+               Statistics_kappa ,
+               Statistics_lambda ,
+               Statistics_entropy )>
+ 
+ 
+<!-- 
+ Number of sequences in BLAST db
+ -->
+<!ELEMENT Statistics_db-num ( %INTEGER; )>
+ 
+<!-- 
+ Length of BLAST db
+ -->
+<!ELEMENT Statistics_db-len ( %INTEGER; )>
+ 
+<!-- 
+ Effective HSP length
+ -->
+<!ELEMENT Statistics_hsp-len ( %INTEGER; )>
+ 
+<!-- 
+ Effective search space
+ -->
+<!ELEMENT Statistics_eff-space ( %REAL; )>
+ 
+<!-- 
+ Karlin-Altschul parameter K
+ -->
+<!ELEMENT Statistics_kappa ( %REAL; )>
+ 
+<!-- 
+ Karlin-Altschul parameter Lambda
+ -->
+<!ELEMENT Statistics_lambda ( %REAL; )>
+ 
+<!-- 
+ Karlin-Altschul parameter H
+ -->
+<!ELEMENT Statistics_entropy ( %REAL; )>
+ 
+ 
+<!-- Definition of Hit -->
+ 
+<!ELEMENT Hit ( 
+               Hit_num ,
+               Hit_id ,
+               Hit_def ,
+               Hit_accession ,
+               Hit_len ,
+               Hit_hsps? )>
+ 
+ 
+<!-- 
+ hit number
+ -->
+<!ELEMENT Hit_num ( %INTEGER; )>
+ 
+<!-- 
+ SeqId of subject
+ -->
+<!ELEMENT Hit_id ( #PCDATA )>
+ 
+<!-- 
+ definition line of subject
+ -->
+<!ELEMENT Hit_def ( #PCDATA )>
+ 
+<!-- 
+ accession
+ -->
+<!ELEMENT Hit_accession ( #PCDATA )>
+ 
+<!-- 
+ length of subject
+ -->
+<!ELEMENT Hit_len ( %INTEGER; )>
+ 
+<!-- 
+ all HSP regions for the given subject
+ -->
+<!ELEMENT Hit_hsps ( Hsp* )>
+ 
+ 
+ 
+<!-- Definition of Hsp -->
+ 
+<!ELEMENT Hsp ( 
+               Hsp_num ,
+               Hsp_bit-score ,
+               Hsp_score ,
+               Hsp_evalue ,
+               Hsp_query-from ,
+               Hsp_query-to ,
+               Hsp_hit-from ,
+               Hsp_hit-to ,
+               Hsp_pattern-from? ,
+               Hsp_pattern-to? ,
+               Hsp_query-frame? ,
+               Hsp_hit-frame? ,
+               Hsp_identity? ,
+               Hsp_positive? ,
+               Hsp_gaps? ,
+               Hsp_align-len? ,
+               Hsp_density? ,
+               Hsp_qseq ,
+               Hsp_hseq ,
+               Hsp_midline? )>
+ 
+ 
+<!-- 
+ HSP number
+ -->
+<!ELEMENT Hsp_num ( %INTEGER; )>
+ 
+<!-- 
+ score (in bits) of HSP
+ -->
+<!ELEMENT Hsp_bit-score ( %REAL; )>
+ 
+<!-- 
+ score of HSP
+ -->
+<!ELEMENT Hsp_score ( %REAL; )>
+ 
+<!-- 
+ e-value of HSP
+ -->
+<!ELEMENT Hsp_evalue ( %REAL; )>
+ 
+<!-- 
+ start of HSP in query
+ -->
+<!ELEMENT Hsp_query-from ( %INTEGER; )>
+ 
+<!-- 
+ end of HSP
+ -->
+<!ELEMENT Hsp_query-to ( %INTEGER; )>
+ 
+<!-- 
+ start of HSP in subject
+ -->
+<!ELEMENT Hsp_hit-from ( %INTEGER; )>
+ 
+<!-- 
+ end of HSP in subject
+ -->
+<!ELEMENT Hsp_hit-to ( %INTEGER; )>
+ 
+<!-- 
+ start of PHI-BLAST pattern
+ -->
+<!ELEMENT Hsp_pattern-from ( %INTEGER; )>
+ 
+<!-- 
+ end of PHI-BLAST pattern
+ -->
+<!ELEMENT Hsp_pattern-to ( %INTEGER; )>
+ 
+<!-- 
+ translation frame of query
+ -->
+<!ELEMENT Hsp_query-frame ( %INTEGER; )>
+ 
+<!-- 
+ translation frame of subject
+ -->
+<!ELEMENT Hsp_hit-frame ( %INTEGER; )>
+ 
+<!-- 
+ number of identities in HSP
+ -->
+<!ELEMENT Hsp_identity ( %INTEGER; )>
+ 
+<!-- 
+ number of positives in HSP
+ -->
+<!ELEMENT Hsp_positive ( %INTEGER; )>
+ 
+<!-- 
+ number of gaps in HSP
+ -->
+<!ELEMENT Hsp_gaps ( %INTEGER; )>
+ 
+<!-- 
+ length of the alignment used
+ -->
+<!ELEMENT Hsp_align-len ( %INTEGER; )>
+ 
+<!-- 
+ score density
+ -->
+<!ELEMENT Hsp_density ( %INTEGER; )>
+ 
+<!-- 
+ alignment string for the query (with gaps)
+ -->
+<!ELEMENT Hsp_qseq ( #PCDATA )>
+ 
+<!-- 
+ alignment string for subject (with gaps)
+ -->
+<!ELEMENT Hsp_hseq ( #PCDATA )>
+ 
+<!-- 
+ formating middle line
+ -->
+<!ELEMENT Hsp_midline ( #PCDATA )>
+ 
+ 
+ 
+ 
diff --git a/network/wwwblast/Src/XML/NCBI_Entity.mod b/network/wwwblast/Src/XML/NCBI_Entity.mod
new file mode 100644
index 00000000..3919c3e8
--- /dev/null
+++ b/network/wwwblast/Src/XML/NCBI_Entity.mod
@@ -0,0 +1,13 @@
+<!-- ======================== -->
+<!-- NCBI DTD                 -->
+<!-- NCBI ASN.1 mapped to XML -->
+<!-- ======================== -->
+ 
+<!-- Entities used to give specificity to #PCDATA -->
+<!ENTITY % INTEGER '#PCDATA'>
+<!ENTITY % ENUM 'EMPTY'>
+<!ENTITY % BOOLEAN 'EMPTY'>
+<!ENTITY % NULL 'EMPTY'>
+<!ENTITY % REAL '#PCDATA'>
+<!ENTITY % OCTETS '#PCDATA'>
+<!-- ============================================ -->
diff --git a/network/wwwblast/Src/XML/blstxml.asn b/network/wwwblast/Src/XML/blstxml.asn
new file mode 100644
index 00000000..1283b986
--- /dev/null
+++ b/network/wwwblast/Src/XML/blstxml.asn
@@ -0,0 +1,120 @@
+--$Id: blstxml.asn,v 1.1 2002/12/02 19:43:46 dondosha Exp $
+--
+--$Revision: 1.1 $
+--**********************************************************************
+--
+--  ASN.1 for simplified BLAST output in XML
+--  by James Ostell, Yuri Wolf and Sergey Shavirin, 2000
+--
+--
+-- $Log: blstxml.asn,v $
+-- Revision 1.1  2002/12/02 19:43:46  dondosha
+-- Copy of the namesake file in distrib/tools CVS directory
+--
+-- Revision 1.1  2002/12/02 19:42:22  dondosha
+-- Copy of the namesake file in distrib/tools CVS directory
+--
+-- Revision 6.7  2002/07/17 22:28:13  dondosha
+-- Added support for megablast XML output
+--
+-- Revision 6.6  2001/05/03 17:52:16  shavirin
+-- Adopted for usage with mani-iterational XML definition.
+--
+-- Revision 6.4  2000/11/08 20:07:20  shavirin
+-- Added new parameter align_len analogos to the number reported in
+-- the Traditional Blast Output.
+--
+-- Revision 6.3  2000/10/23 20:24:03  shavirin
+-- Few parameters were changed to OPTIONAL to allow XML without results:
+-- failure or no hits found condition.
+--
+-- Revision 6.2  2000/08/11 17:48:35  shavirin
+-- Small fix.
+--
+-- Revision 6.1  2000/08/09 20:43:12  shavirin
+-- Initial revision.
+--
+--
+--**********************************************************************
+
+NCBI-BlastOutput DEFINITIONS ::=
+BEGIN
+
+BlastOutput ::= SEQUENCE {
+	program VisibleString ,		-- BLAST program: blastp, tblastx etc.
+	version VisibleString ,		-- Program version 
+	reference VisibleString ,	-- Steven, David, Tom and others
+	db VisibleString ,		-- BLAST Database name
+	query-ID VisibleString ,	-- SeqId of query
+	query-def VisibleString ,	-- Definition line of query
+	query-len INTEGER ,		-- length of query sequence
+	query-seq VisibleString OPTIONAL ,	-- query sequence itself
+	param Parameters,		-- search parameters
+        iterations SEQUENCE OF Iteration,
+        mbstat Statistics OPTIONAL        -- Mega BLAST search statistics
+}
+Iteration ::= SEQUENCE {
+	iter-num INTEGER ,	         -- iteration number
+	query-ID VisibleString OPTIONAL, -- SeqId of query
+	query-def VisibleString OPTIONAL,-- Definition line of query
+	query-len INTEGER OPTIONAL ,	 -- length of query sequence
+	hits SEQUENCE OF Hit OPTIONAL,	 -- Hits one for every db sequence
+	stat Statistics OPTIONAL,	 -- search statistics            
+        message VisibleString OPTIONAL   -- Some (error?) information
+}
+Parameters ::= SEQUENCE {
+	matrix VisibleString OPTIONAL ,	-- Matrix used (-M)
+	expect REAL ,			-- Expectation threshold (-e)
+	include REAL OPTIONAL ,		-- Inclusion threshold (-h)
+	sc-match INTEGER OPTIONAL ,	-- match score for NT (-r)
+	sc-mismatch INTEGER OPTIONAL ,	-- mismatch score for NT (-q)
+	gap-open INTEGER ,		-- Gap opening cost (-G)
+	gap-extend INTEGER ,		-- Gap extension cost (-E)
+	filter VisibleString OPTIONAL,  -- Filtering options (-F)
+	pattern VisibleString OPTIONAL,	-- PHI-BLAST pattern
+        entrez-query VisibleString OPTIONAL -- Limit of request to Entrez query
+}
+	
+Statistics ::= SEQUENCE {
+	db-num INTEGER ,		-- Number of sequences in BLAST db
+	db-len INTEGER ,		-- Length of BLAST db
+	hsp-len INTEGER ,		-- Effective HSP length
+	eff-space REAL,			-- Effective search space
+        kappa REAL,                     -- Karlin-Altschul parameter K
+        lambda REAL,                    -- Karlin-Altschul parameter Lambda
+        entropy REAL                    -- Karlin-Altschul parameter H
+}       
+
+Hit ::= SEQUENCE {
+	num INTEGER ,			-- hit number
+	id VisibleString ,		-- SeqId of subject
+	def VisibleString ,		-- definition line of subject
+	accession VisibleString ,       -- accession
+	len INTEGER ,			-- length of subject
+	hsps SEQUENCE OF Hsp OPTIONAL	-- all HSP regions for the given subject
+}
+
+Hsp ::= SEQUENCE {
+	num INTEGER ,			-- HSP number
+	bit-score REAL ,		-- score (in bits) of HSP
+	score REAL ,			-- score of HSP
+	evalue REAL ,			-- e-value of HSP
+	query-from INTEGER ,		-- start of HSP in query
+	query-to INTEGER ,		-- end of HSP
+	hit-from INTEGER,		-- start of HSP in subject
+	hit-to INTEGER ,		-- end of HSP in subject
+	pattern-from INTEGER OPTIONAL ,	-- start of PHI-BLAST pattern
+	pattern-to INTEGER OPTIONAL ,	-- end of PHI-BLAST pattern
+	query-frame INTEGER OPTIONAL ,	-- translation frame of query
+	hit-frame INTEGER OPTIONAL ,	-- translation frame of subject
+	identity INTEGER OPTIONAL ,	-- number of identities in HSP
+	positive INTEGER OPTIONAL ,	-- number of positives in HSP
+	gaps INTEGER OPTIONAL ,		-- number of gaps in HSP
+	align-len INTEGER OPTIONAL ,	-- length of the alignment used
+	density INTEGER OPTIONAL ,	-- score density
+	qseq VisibleString ,		-- alignment string for the query (with gaps)
+	hseq VisibleString,		-- alignment string for subject (with gaps)
+	midline VisibleString OPTIONAL	-- formating middle line
+}
+
+END
diff --git a/network/wwwblast/Src/bl2bag.c b/network/wwwblast/Src/bl2bag.c
new file mode 100644
index 00000000..c96dff49
--- /dev/null
+++ b/network/wwwblast/Src/bl2bag.c
@@ -0,0 +1,466 @@
+/* $Id: bl2bag.c,v 1.3 2003/07/15 19:57:11 coulouri Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: bl2bag.c,v $
+*
+* Initial Creation Date: 10/23/2000
+*
+* $Revision: 1.3 $
+*
+* File Description:
+*        BLAST 2 Sequences CGI program for some drawing
+*
+* $Log: bl2bag.c,v $
+* Revision 1.3  2003/07/15 19:57:11  coulouri
+* use sigaction()
+*
+* Revision 1.2  2003/05/09 21:09:04  dondosha
+* Removed unused variables
+*
+* Revision 1.1  2002/12/02 18:05:53  dondosha
+* Moved from different locations to a common one
+*
+* Revision 6.4  2002/08/06 21:32:59  dondosha
+* Added sys/resource.h include for rlimit
+*
+* Revision 6.3  2002/08/06 21:26:25  dondosha
+* Changed exit to return in Main
+*
+* Revision 6.2  2000/11/03 16:37:09  shavirin
+* Added standrard header and started logging.
+*
+*
+* ==========================================================================
+*/
+
+#include <signal.h>
+#include <ncbi.h>
+#include <asn.h>
+
+#include <ncbigif.h>
+#include <gifgen.h>
+#include <sys/resource.h>
+
+typedef struct {
+	CharPtr tag;
+	CharPtr val;
+} TAG;
+
+static TAG tag[] = {
+	{ NULL, NULL }
+};
+
+static TAG empty_utag = { NULL, NULL };
+static Int4 nutag = 1;
+static TAG *utag = &empty_utag;
+
+TAG *get_utag(void)
+{
+	return utag;
+}
+
+static void content(void)
+{
+	static Boolean was = FALSE;
+
+	if (was) {
+		return;
+	}
+	printf("Content-type: text/html\n\n");
+	was = TRUE;
+}
+
+static void AbortPage(CharPtr mess)
+{
+	content();
+	printf("<TITLE>ERROR</TITLE>\n");
+		printf("<h2>\n");
+	printf("<img src=images/confused.gif align=middle>\n");
+	printf("%s</h2>\n", mess);
+	exit(1);
+}
+
+static Int4 hexdigit(Char c)
+{
+   switch (c) {
+   default: return 0;
+   case '0': return 0;
+   case '1': return 1;
+   case '2': return 2;
+   case '3': return 3;
+   case '4': return 4;
+   case '5': return 5;
+   case '6': return 6;
+   case '7': return 7;
+   case '8': return 8;
+   case '9': return 9;
+   case 'a':
+   case 'A': return 10;
+   case 'b':
+   case 'B': return 11;
+   case 'c':
+   case 'C': return 12;
+   case 'd':
+   case 'D': return 13;
+   case 'e':
+   case 'E': return 14;
+   case 'f':
+   case 'F': return 15;
+   }
+}
+
+static void TimeExpired(Int4 i)
+{
+	content();
+	printf("<HTML>\n");
+	printf("<HEAD>\n");
+	printf("<TITLE>\n");
+	printf("Time Expired\n");
+	printf("</TITLE>\n");
+	printf("</HEAD>\n");
+	printf("<BODY>\n");
+	printf("<H1>\n");
+	/*printf("<img src=/IMAGE/time-exp.gif align=middle hspace=21>\n");*/
+	printf("Time expired\n");
+	printf("</H1>\n");
+	printf("<HR>\n");
+	printf("</BODY>\n");
+	printf("</HTML>\n");
+	exit(0);
+}
+
+void fill_tag(CharPtr str, TAG *tag)
+{
+	Int4 i, l;
+	CharPtr s;
+	TAG *buftag;
+
+	for (i=0; tag[i].tag != NULL; i++) {
+		l = strlen(tag[i].tag);
+		if (strncmp(tag[i].tag, str, l) == 0) {
+			str += l;
+			for (s = str, l = 0; *s != '\0' && *s != '&'; s++) {
+				if (!IS_WHITESP(*s)) {
+					l++;
+				}
+			}
+			if (l > 0) {
+				tag[i].val = str;
+			}
+			return;
+		}
+	}
+	if ((buftag = (TAG *)MemNew((nutag+1) * sizeof(utag[0]))) == NULL)
+           AbortPage("Not enough memory");
+        
+	if (nutag > 1) {
+		MemCpy(buftag, utag, nutag * sizeof(utag[0]));
+	/*	free(utag);*/
+	}
+	utag = buftag;
+	buftag = utag + nutag - 1;
+	buftag->tag = str;
+	for (s = str; *s != '\0' && *s != '='; s++) ;
+	if (*s == '=') {
+		*s++ = '\0';
+		buftag->val = s;
+	}
+	buftag[1].tag = NULL;
+	buftag[1].val = NULL;
+	nutag++;
+}
+
+void get_str_tag(CharPtr str, TAG *tag)
+{
+	CharPtr s, beg;
+        Char c;
+	Int4 i1, i2;
+
+	beg = str;
+	for (s = str; *s != '\0'; s++) {
+		if (*s == '+') {
+			*s = ' ';
+		} else if (*s == '&') {
+			fill_tag(beg, tag);
+			beg = s + 1;
+			*s = '\0';
+		} else if (*s == '%') {
+			i1 = hexdigit(s[1]);
+			i2 = hexdigit(s[2]);
+			c = (i1 << 4) + i2;
+			if (c == '\r') {
+				strcpy(s, s+3);
+				s--;
+			} else {
+				strcpy(s+1, s+3);
+				*s = c;
+			}
+		}
+	}
+	fill_tag(beg, tag);
+}
+
+/* RLIMIT_CPU      The maximum amount of CPU  time  in  seconds
+                     used  by  a  process.   This is a soft limit */
+#define limitCPU 300;
+
+Int4 get_tag(tag, method)
+TAG tag[];
+CharPtr method;
+{
+	Int4 n;
+	CharPtr str;
+	static Char buf[133];
+	struct sigaction sa;
+	sigset_t sigset;
+	struct rlimit rl;
+
+	getrlimit(RLIMIT_CPU, &rl);
+	rl.rlim_cur = limitCPU;
+	rl.rlim_max = rl.rlim_cur + 30;
+
+	setrlimit(RLIMIT_CPU, &rl);
+
+	sigfillset(&sigset);
+	sa.sa_mask = sigset;
+	sa.sa_flags = SA_RESETHAND | SA_RESTART;
+	sa.sa_handler = TimeExpired;
+	sigaction(SIGXCPU, &sa, NULL);
+
+	str = getenv("REQUEST_METHOD");
+	if (str == NULL) {
+		return FALSE;
+	}
+	if (method == NULL) {
+		method = str;
+	}
+	if (StringCmp(method, "POST") == 0) {
+		if (StringCmp(str, "POST") != 0) {
+			sprintf(buf, "Not a METHOD of POST (%s).", str);
+                        AbortPage(buf);
+		}
+		str = getenv("CONTENT_TYPE");
+		if (str == NULL) {
+			sprintf(buf, "No CONTENT_TYPE");
+			AbortPage(buf);
+		}
+		if (StringCmp(str, "application/x-www-form-urlencoded") != 0) {
+			sprintf(buf, "Wrong CONTENT_TYPE: (%s).", str);
+                        AbortPage(buf);
+		}
+		if ((n = atoi(getenv("CONTENT_LENGTH"))) <= 0) {
+			    AbortPage("No arguments");
+		}
+		if ((str = (CharPtr)MemNew((n + 1)*sizeof(Char))) == NULL)
+                   AbortPage("Not enough memory");
+		if (fread(str, 1, n, stdin) != n) {
+			AbortPage("Arguments were not transfered correctly");
+		}
+	} else if (StringCmp(method, "GET") == 0) {
+		if (StringCmp(str, "GET") != 0) {
+			sprintf(buf, "Not a METHOD of GET (%s).", str);
+			    AbortPage(buf);
+		}
+		str = getenv("QUERY_STRING");
+		if (str == NULL) {
+			AbortPage("No query information to decode");
+		}
+	} else {
+		sprintf(str, "Bad requested method: %s", method);
+		AbortPage(str);
+	}
+	get_str_tag(str, tag);
+	return TRUE;
+}
+
+static gdImagePtr GIF;
+
+#define WIDTH    28
+#define HEIGHT   28
+
+static Int4 height = 100, width=100;
+
+static Int4 dig62(char c)
+{
+	Int4 num;
+
+	num = isdigit(c) ? c-'0' :
+		isupper(c) ? c-'A'+10 :
+		islower(c) ? c-'a'+36 : 0;
+	return num;
+}
+
+static Int4 sym2num(CharPtr PNTR ps)
+{
+	Int4 num;
+	CharPtr s = *ps;
+
+	num = dig62(*s++) * 62;
+	num += dig62(*s++);
+	*ps = s;
+	return num;
+}
+
+static Int4 hex1(char c)
+{
+	return isdigit(c) ? c-'0' :
+			isupper(c) ? c-'A'+10 :
+			islower(c) ? c-'a'+10 : 0;
+}
+
+static Int4 hex2(CharPtr s)
+{
+	return hex1(s[0]) * 16 +  hex1(s[1]);
+}
+
+static void dxy2point(po, x, y)
+gdPoint *po;
+FloatHi x, y;
+{
+	po->x = x + .5;
+	po->y = y + .5;
+}
+
+static void xy2point(po, x, y)
+gdPoint *po;
+Int4 x, y;
+{
+	po->x = x;
+	po->y = y;
+}
+
+Int2 Main(void)
+{
+	CharPtr s, str;
+	TAG *utag;
+	Int4 x1, x2, y1, y2, w, xw, yw;
+	Int4 col1, col2, col3, colw, colb, colp;
+	FloatHi al, wsin, wcos;
+	Int4 rect, six;
+	static gdPoint po[6];
+
+	get_tag(tag, NULL);
+	utag = get_utag();
+	for (; utag->tag != NULL && utag->tag[0] == '\0'; utag++) ;
+	if ((str = utag->tag) == NULL) {
+		AbortPage("No arguments");
+	}
+	s = str;
+	width = sym2num(&s);
+	height = sym2num(&s);
+	if (*s == '-') {
+		s++;
+		if ((GIF = gdImageCreate(width, height)) == NULL) {
+			AbortPage("No memory to create picture");
+		}
+		colw = gdImageColorAllocate(GIF, 255, 255, 255);
+		gdImageColorTransparent(GIF, colw);
+	} else {
+		col1 = hex2(s+0);
+		col2 = hex2(s+2);
+		col3 = hex2(s+4);
+		s += 7;
+		if ((GIF = gdImageCreate(width, height)) == NULL) {
+			AbortPage("No memory to create picture");
+		}
+		colw = gdImageColorAllocate(GIF, col1, col2, col3);
+	}
+	colb = gdImageColorAllocate(GIF, 1, 1, 1);
+	gdImageFilledRectangle(GIF, 0, 0, width-1, height-1, colw);
+	gdImageRectangle(GIF, 0, 0, width-1, height-1, colb);
+	do {
+		rect = FALSE;
+		six = FALSE;
+		if (*s == 'r') {
+			rect = TRUE;
+			s++;
+		} else if (*s == 's') {
+			six = TRUE;
+			s++;
+		}
+		if (*s == '(') {
+			AbortPage("Bad format (no color)");
+		} else {
+			col1 = hex2(s);
+			col2 = hex2(s+2);
+			col3 = hex2(s+4);
+			s += 6;
+		}
+		colp = gdImageColorAllocate(GIF, col1, col2, col3);
+		if (isdigit(*s)) {
+			w = atoi(s);
+			for (; isdigit(*s); s++) ;
+		} else {
+			w = 0;
+		}
+		if (*s == '(') {
+			s++;
+		} else {
+			AbortPage("Bad format (no '(')");
+		}
+		if (*s != ')') {
+			do {
+				x1 = sym2num(&s);
+				y1 = sym2num(&s);
+				x2 = sym2num(&s);
+				y2 = sym2num(&s);
+				al = atan2((FloatHi) (y2-y1), (FloatHi) (x2-x1));
+				wsin = w * sin(al);
+				wcos = w * cos(al);
+				if (rect) {
+					gdImageFilledRectangle(GIF, x1, y1, x2, y2, colp);
+					for (; w > 0; w--) {
+						gdImageRectangle(GIF, x1-w, y1-w, x2+w, y2+w, colb);
+					}
+				} else if (six) {
+					xw = (x1 < x2) ? w : -w;
+					yw = (y1 < y2) ? w : -w;
+					xy2point(po  , x1   , y1   );
+					xy2point(po+1, x1+xw, y1   );
+					xy2point(po+2, x2   , y2-yw);
+					xy2point(po+3, x2   , y2   );
+					xy2point(po+4, x2-xw, y2   );
+					xy2point(po+5, x1   , y1+yw);
+					gdImageFilledPolygon(GIF, po, 6, colp);
+				} else if (w == 0) {
+					gdImageLine(GIF, x1, y1, x2, y2, colp);
+				} else {
+					dxy2point(po  , x1 - wsin, y1 + wcos);
+					dxy2point(po+1, x1 + wsin, y1 - wcos);
+					dxy2point(po+2, x2 + wsin, y2 - wcos);
+					dxy2point(po+3, x2 - wsin, y2 + wcos);
+					gdImageFilledPolygon(GIF, po, 4, colp);
+					gdImagePolygon(GIF, po, 4, colb);
+				}
+			} while (*s != ')' && *s != '\0') ;
+		}
+		if (*s != '\0') {
+			s++;
+		}
+	} while (*s != '\0') ;
+	printf("Content-type: image/gif\n\n");
+	gdImageGif(GIF, stdout);
+	return 0;
+}
diff --git a/network/wwwblast/Src/psiblast.c b/network/wwwblast/Src/psiblast.c
new file mode 100644
index 00000000..c192d0a3
--- /dev/null
+++ b/network/wwwblast/Src/psiblast.c
@@ -0,0 +1,418 @@
+/* $Id: psiblast.c,v 1.3 2003/07/15 19:57:11 coulouri Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: psiblast.c,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 04/21/2000
+*
+* $Revision: 1.3 $
+*
+* File Description:
+*         WWW PSI BLAST Main file
+*
+* $Log: psiblast.c,v $
+* Revision 1.3  2003/07/15 19:57:11  coulouri
+* use sigaction()
+*
+* Revision 1.2  2003/05/09 21:09:04  dondosha
+* Removed unused variables
+*
+* Revision 1.1  2002/08/06 19:18:53  dondosha
+* Source for WWW BLAST server, initial revision.
+*
+* Revision 6.6  2000/11/03 20:38:41  shavirin
+* Minor formating change.
+*
+* Revision 6.5  2000/10/31 20:19:39  shavirin
+* Added printing progeress messages to avoid browser timeout.
+*
+* Revision 6.4  2000/08/10 18:18:26  shavirin
+* Fixed problem with printing PHI Blast output.
+*
+* Revision 6.3  2000/08/10 14:40:50  shavirin
+* Fixed typo.
+*
+* Revision 6.2  2000/08/09 20:32:18  shavirin
+* Added hidden printing of posFreqs encoded array.
+*
+* Revision 6.1  2000/05/17 15:49:40  shavirin
+* Initial revision.
+*
+*
+* ==========================================================================
+*/
+
+#include <signal.h>
+#include <wwwblast.h>
+
+static CharPtr non_printed_tag[] = { "PSI_MATRIX", "PHI_PATTERN", 
+                                     "checked_GI", "PSI_KARLIN_K",
+                                     "PHI_BLAST", "defline", "NEXT_I",
+                                     "E_THRESH", "STEP_NUMBER", NULL
+};
+
+#define DEFAULT_ETHRESH "0.001"
+
+static void SigAlrmHandler(int i)
+{
+    i = 0;
+}
+
+/*
+  Formats the evalue and bit_score in a standard way.
+*/
+
+static Int4 Sip2GI(SeqIdPtr sip)
+{
+    SeqIdPtr	sip_tmp;
+    
+    for(sip_tmp = sip; sip_tmp != NULL; sip_tmp = sip_tmp->next) {
+	if(sip_tmp->choice == SEQID_GI) {
+	    return sip_tmp->data.intvalue;
+	}
+    }
+    return 0;
+}
+
+static void PSIPrintHiddenData(WWWInfoPtr info, Boolean is_phi_blast)
+{
+    Int4 i, j, number;
+    CharPtr chptr;
+    Boolean found;
+
+    number = WWWGetNumEntries(info);
+
+    for(i = 0; i < number; i++) {
+        
+        chptr = WWWGetNameByIndex(info, i);
+        
+        for(j = 0, found = FALSE; non_printed_tag[j] != NULL; j++) {
+            if(!StringICmp(non_printed_tag[j], chptr)) {
+		if(!StringICmp("PHI_PATTERN", chptr) && is_phi_blast)
+                    found = FALSE;
+                else {
+                    found = TRUE;
+                    break;
+                }
+            }
+        }
+        if(!found) {
+	    fprintf(stdout, "<INPUT TYPE=\"hidden\" "
+                    "NAME= \"%s\" VALUE=\"%s\">\n",
+		    WWWGetNameByIndex(info, i), 
+		    WWWGetValueByIndex(info, i));
+	}
+    }
+    return;
+}
+
+static Boolean  TestConvergence(GIListPtr good, GIListPtr checked, 
+	SeqAlignPtr goodseqaligns, SeqAlignPtr badseqaligns, Int2Ptr marks)
+{
+    Int4		gi;
+    SeqAlignPtr 	gsl = goodseqaligns;
+    SeqIdPtr		sip;
+    Boolean		retval = TRUE, found;
+    GIListPtr		gil = NULL;
+    Int4		count;
+    
+    if(goodseqaligns == NULL) {
+	return FALSE; 
+    }
+    /* Fill in marks list */
+
+    for (gsl = goodseqaligns, count = 0; gsl; gsl = gsl->next, count++) {
+    
+	marks[count] = (Int2) 0;
+
+	/* get SeqIdPtr using SeqAlignPtr */
+	sip = TxGetSubjectIdFromSeqAlign(gsl);
+
+	/* get GI from SeqIdPtr */
+	gi = Sip2GI(sip);
+
+
+	/* check if this gi presents in the list of previous cheched GI's */
+	found = FALSE;
+	for (gil = checked; !found && gil; gil = gil->next) {
+	    if (gil->gi == gi) {
+		found = TRUE;
+		marks[count] += SEQ_ALIGN_MARK_PREVCHECKED;
+	    }
+	}
+
+	/* check if this gi presents in the list of previous Good GI's */
+	found = FALSE;
+	for (gil = good; !found && gil; gil = gil->next) {
+	    if (gil->gi == gi) {
+		found = TRUE;
+		marks[count] += SEQ_ALIGN_MARK_PREVGOOD;
+	    }
+	}
+    }
+
+    for (gsl = badseqaligns; gsl; gsl = gsl->next, count++) {
+    
+	marks[count] = (Int2) SEQ_ALIGN_MARK_PREVGOOD;
+
+	/* get SeqIdPtr using SeqAlignPtr */
+	sip = TxGetSubjectIdFromSeqAlign(gsl);
+
+	/* get GI from SeqIdPtr */
+	gi = Sip2GI(sip);
+
+
+	/* check if this gi presents in the list of previous cheched GI's */
+	found = FALSE;
+	for (gil = checked; !found && gil; gil = gil->next) {
+	    if (gil->gi == gi) {
+		found = TRUE;
+		marks[count] += SEQ_ALIGN_MARK_PREVCHECKED;
+	    }
+	}
+    }
+    /* marks is built, now scan needed lists and figure out if process is converged */
+
+    /* Important:  Convergence is now defined as follows:
+       Each seq which is good now, should have been checked on previous iteration
+       */
+
+    retval = TRUE;
+    for (gsl = goodseqaligns, count = 0;
+	    retval && gsl; gsl = gsl->next, count++) {
+    
+	/* get SeqIdPtr using SeqAlignPtr */
+	sip = TxGetSubjectIdFromSeqAlign(gsl);
+
+	/* get GI from SeqIdPtr */
+	gi = Sip2GI(sip);
+
+	if (!(marks[count] & SEQ_ALIGN_MARK_PREVCHECKED))
+	    retval = FALSE;
+    }
+    return retval;
+}
+
+Int2 Main (void)
+ 
+{
+    WWWBlastInfoPtr theInfo;
+    BLASTPrintDataPtr	print_data;
+    PSIDataPtr		psidata; 
+    Nlm_FloatHi		ethresh_old;
+    Boolean		isConverged;
+    SeqAlignPtr		BadSeqAlignments, GoodSeqAlignments, lastGood = NULL;
+    Int2		countGood, countBad;
+    Int2Ptr		marks;
+    struct sigaction sa;
+    sigset_t sigset;
+
+    sigfillset(&sigset);
+    sa.sa_mask = sigset;
+
+    sa.sa_flags = SA_RESTART;
+    sa.sa_handler = SigAlrmHandler;
+    sigaction(SIGALRM, &sa, NULL);
+    sigaction(SIGPIPE, &sa, NULL);
+    
+    UseLocalAsnloadDataAndErrMsg ();
+
+    if (! SeqEntryLoad()) {
+        fprintf(stdout, "Cannot read NCBI DATA directory\n");
+        return 1;
+    }
+    
+    /* This function will read posting data, set-up config file and
+       write small message into logfile (if it exists) */
+    
+    if((theInfo = WWWBlastReadArgs(NULL)) == NULL)
+        return 1;
+
+    /* Read options into structure */
+    if(!WWWCreateSearchOptions(theInfo)) {
+        return 1;
+    }
+
+    /* validate them */
+    if(!WWWValidateOptions(theInfo)) {
+        return 1;
+    }
+    if (theInfo->options->ethresh == 0.0)
+        theInfo->options->ethresh = atof(DEFAULT_ETHRESH);
+    
+    if (theInfo->is_phi_blast == FALSE) {
+        if((print_data = PSIBlastSearch(theInfo)) == NULL ||
+           print_data->seqalign == NULL) {
+            fprintf(stdout, "<PRE>\n");
+            fprintf(stdout, "\n\nNo hit found...\n\n");
+
+            if(print_data != NULL) {
+                
+                /* We will print bottom of the page eventually */
+                init_buff();
+
+                if (print_data->ka_params_gap) {
+                    PrintKAParameters(print_data->ka_params_gap->Lambda, 
+                                      print_data->ka_params_gap->K, 
+                                      print_data->ka_params_gap->H, 
+                                      70, stdout, TRUE);
+                }
+
+                PrintTildeSepLines(print_data->buffer, 70, stdout);
+                free_buff();
+            }
+            fprintf(stdout, "</PRE></BODY></HTML>\n");
+
+            FileClose(stdout);
+            return(0);
+        }
+    } else {
+        /* PHI Blast can work only with 1 CPU ;-))) */
+	theInfo->options->number_of_cpus = 1;
+    	if((print_data = PHIBlastSearch(theInfo)) == NULL ||
+           print_data->vnp == NULL || print_data->seqloc == NULL) {
+
+            fprintf(stdout, "<PRE>\n");
+            fprintf(stdout, "\n<BR>No hit found...<BR>\n");
+            
+            if(print_data != NULL) {
+                
+                /* We will print bottom of the page eventually */
+                init_buff();                
+                if (print_data->ka_params_gap) {                
+                    PrintKAParameters(print_data->ka_params_gap->Lambda, 
+                                      print_data->ka_params_gap->K, 
+                                      print_data->ka_params_gap->H, 
+                                      70, stdout, TRUE);
+                }
+                
+                PrintTildeSepLines(print_data->buffer, 70, stdout);
+                free_buff();
+            }
+
+            fprintf(stdout, "</PRE></BODY></HTML>\n");
+
+            FileClose(stdout);
+            return(0);
+        }
+    }
+
+    /* At this point we have non-NULL seqalign and therefore can 
+       print some results out */
+    
+    if((psidata = print_data->psidata) == NULL) {
+        WWWBlastErrMessage(BLASTMiscError, NULL);
+        BLASTPrintDataFree(print_data); 
+        WWWBlastInfoFree(theInfo);
+        return 1;
+    }
+    
+    ethresh_old = theInfo->options->ethresh;
+    
+    if (theInfo->options->ethresh == 0.0)
+    	ethresh_old = atof(DEFAULT_ETHRESH);
+    
+    isConverged = FALSE;
+    if (theInfo->is_phi_blast == FALSE) {
+        SplitSeqAlign(print_data->seqalign, &GoodSeqAlignments, 
+                      &BadSeqAlignments, &lastGood, &marks, 
+                      &countBad, &countGood, ethresh_old);
+        
+        isConverged = TestConvergence(psidata->PrevGoodGIs, 
+                                      psidata->PrevCheckedGIs, 
+                                      GoodSeqAlignments, 
+                                      BadSeqAlignments, marks);
+    }
+    
+    fprintf(stdout, "<FORM NAME=\"PSI_BLAST\" METHOD=\"POST\" "
+            "ACTION=\"%s/step%d\" ENCTYPE= \"multipart/form-data\">\n", 
+            getenv("SCRIPT_NAME") == NULL ? "" : getenv("SCRIPT_NAME"),
+            /* WWWGetPort(theInfo->info), */ psidata->StepNumber);
+    
+    if(isConverged) {
+        fprintf(stdout, "<FONT color=\"blue\">"
+                "<HR><CENTER><b><h1>Converged !!!</h1></b></CENTER>"
+                "</FONT><p>");
+    }
+    
+    fprintf(stdout, "<HR>");
+    
+    fprintf(stdout, "<PRE><a href=\"#Evalue\">E-value</a> threshold for inclusion in PSI-Blast iteration %d: %lg <BR>", psidata->StepNumber+1, ethresh_old);
+    fprintf(stdout, "E-value threshold for inclusion in PSI-Blast iteration %d: ", psidata->StepNumber+2);
+    fprintf(stdout, "<INPUT TYPE=\"text\" NAME=\"E_THRESH\" VALUE=\"%lg\" MAXLENGTH=\"10\">\r", ethresh_old);
+    
+    fprintf(stdout, "<HR>\r");             
+    fprintf(stdout, "<BR><BR>");   
+
+    fprintf(stdout, "<INPUT TYPE=\"hidden\" NAME =\"STEP_NUMBER\" VALUE =\"%d\">\n", 
+	    psidata->StepNumber+1);
+
+    if (psidata->StepNumber > 0)
+	fprintf(stdout, "<HR><CENTER><b> Results of PSI-Blast iteration %d</b></CENTER>\n", psidata->StepNumber);
+    
+    fflush(stdout);
+    
+    if (theInfo->is_phi_blast == FALSE) {
+	PSIPrintOutput(theInfo, print_data, BadSeqAlignments, 
+                       GoodSeqAlignments, lastGood, marks, countBad, 
+                       countGood, ethresh_old);
+    } else {
+	PHIPrintOutput(theInfo, print_data, print_data->vnp, ethresh_old);
+    }
+
+    MemFree(marks);
+
+    fprintf(stdout, "</PRE>\n");
+    
+    if (psidata->StepNumber > 0) {
+        fprintf(stdout, "<INPUT TYPE=\"hidden\" "
+                "NAME= \"PSI_MATRIX\" VALUE = \"%s\">\n", 
+                psidata->matrix62);
+        fprintf(stdout, "<INPUT TYPE=\"hidden\" "
+                "NAME= \"POS_FREQS\" VALUE = \"%s\">\n", 
+                psidata->CHARPosFreqs); 
+        fprintf(stdout, "<INPUT TYPE=\"hidden\" "
+                "NAME= \"PSI_KARLIN_K\" VALUE = \"%lf\">", psidata->karlinK);
+    }
+    
+    PSIPrintHiddenData(theInfo->info, theInfo->is_phi_blast);
+    
+    fprintf(stdout, "</FORM>");
+
+    if (theInfo->is_phi_blast == FALSE) {
+        print_data->seqalign = NULL;     
+        SeqAlignSetFree(GoodSeqAlignments);
+        SeqAlignSetFree(BadSeqAlignments);
+    }
+
+    BLASTPrintDataFree(print_data); 
+    WWWBlastInfoFree(theInfo);
+
+    fflush(stdout);
+    return 0;
+}
+
diff --git a/network/wwwblast/Src/viewgif.c b/network/wwwblast/Src/viewgif.c
new file mode 100644
index 00000000..1eded844
--- /dev/null
+++ b/network/wwwblast/Src/viewgif.c
@@ -0,0 +1,97 @@
+#include <signal.h>
+#include <fcntl.h>
+#include <stdio.h>
+
+static void SigAlrmHandler(int);
+static void SigTermHandler(int);
+
+static char FileName[128];
+
+main(void) 
+{
+    FILE *pp;
+    char tmp_buff[1024];
+    char *PidFile;
+
+    int  bytes;
+    char *ContentGif  =  "Content-type: image/gif\r\n\r\n";
+    struct sigaction sa;
+    sigset_t sigset;
+
+    sigfillset(&sigset);
+    sa.sa_mask = sigset;
+
+    sa.sa_flags = SA_RESETHAND | SA_RESTART;
+    sa.sa_handler = SigAlrmHandler;
+    sigaction(SIGALRM, &sa, NULL);
+
+    sa.sa_handler = SigTermHandler;
+    sigaction(SIGTERM, &sa, NULL);
+    sigaction(SIGPIPE, &sa, NULL);
+    
+    PidFile = (char *) getenv("QUERY_STRING"); 
+    
+    sprintf(FileName, "TmpGifs/%s", PidFile);
+    
+    if((pp = fopen(FileName, "r")) == NULL) {
+
+        /* Just do nothing */
+        sprintf(tmp_buff, "HTTP/1.0 204 Not Modified\n");
+        write(1, tmp_buff, strlen(tmp_buff));
+        sprintf(tmp_buff, "Server: %s\n", (char *) getenv("SERVER_SOFTWARE"));
+        write(1, tmp_buff, strlen(tmp_buff));
+        sprintf(tmp_buff, "MIME-Version: 1.0\n");
+        write(1, tmp_buff, strlen(tmp_buff));
+        write(1, ContentGif, strlen(ContentGif)); 
+    } else {
+        sprintf(tmp_buff, "HTTP/1.0 200 OK\r\n");
+        write(1, tmp_buff, strlen(tmp_buff));
+        sprintf(tmp_buff, "Server: %s\n", (char *) getenv("SERVER_SOFTWARE"));
+        write(1, tmp_buff, strlen(tmp_buff));
+        sprintf(tmp_buff, "MIME-Version: 1.0\r\n");
+        write(1, tmp_buff, strlen(tmp_buff));
+        write(1, ContentGif, strlen(ContentGif)); 
+        
+        while ((bytes =fread(tmp_buff, 1, 256, pp)) >0)
+            write(1, tmp_buff, bytes); 
+    }
+    remove(FileName); 
+    return 0;
+}
+static void SigAlrmHandler(int id)
+{
+    
+    char tmp_buff[1024];
+    char *ContentGif  =  "Content-type: image/gif\r\n\r\n";
+    
+    sprintf(tmp_buff, "HTTP/1.0 204 Not Modified\n");
+    write(1, tmp_buff, strlen(tmp_buff));
+    sprintf(tmp_buff, "Server: %s\n", (char *) getenv("SERVER_SOFTWARE"));
+    write(1, tmp_buff, strlen(tmp_buff));
+    sprintf(tmp_buff, "MIME-Version: 1.0\n");
+    write(1, tmp_buff, strlen(tmp_buff));
+    write(1, ContentGif, strlen(ContentGif)); 
+    remove(FileName); 
+    exit(1);   
+}
+
+static void SigTermHandler(int id)
+{
+    remove(FileName); 
+    exit(1);
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/network/wwwblast/Src/wblast2.c b/network/wwwblast/Src/wblast2.c
new file mode 100644
index 00000000..e0270302
--- /dev/null
+++ b/network/wwwblast/Src/wblast2.c
@@ -0,0 +1,2996 @@
+/* $Id: wblast2.c,v 1.7 2003/07/14 18:43:17 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: wblast2.c,v $
+*
+* Initial Creation Date: 10/23/2000
+*
+* $Revision: 1.7 $
+*
+* File Description:
+*        BLAST 2 Sequences CGI program
+*
+* $Log: wblast2.c,v $
+* Revision 1.7  2003/07/14 18:43:17  dondosha
+* Changed Entrez references syntax
+*
+* Revision 1.6  2003/07/01 20:32:59  dondosha
+* Fix in javascript for matrix and strand menus when program is changed
+*
+* Revision 1.5  2003/07/01 16:33:55  dondosha
+* Changed logging; corrected CPU limit handling for Linux
+*
+* Revision 1.4  2003/05/09 22:12:25  dondosha
+* Corrections for Darwin compilation
+*
+* Revision 1.3  2003/05/09 21:09:04  dondosha
+* Removed unused variables
+*
+* Revision 1.2  2002/12/02 22:40:19  dondosha
+* Changed uint64_t to a portable Uint8
+*
+* Revision 1.1  2002/12/02 18:05:53  dondosha
+* Moved from different locations to a common one
+*
+* Revision 6.34  2002/12/02 17:58:30  dondosha
+* No logging or connection thread for standalone WWW server version
+*
+* Revision 6.33  2002/10/04 21:24:55  dondosha
+* 1. Added logging;
+* 2. Added user disconnect handling: SIGPIPE, plus a poll thread to detect disconnection while nothing is yet being returned to the browser.
+*
+* Revision 6.32  2002/09/24 15:48:59  dondosha
+* Changed path to standalone executables ftp site
+*
+* Revision 6.31  2002/09/04 20:13:37  dondosha
+* Corrected the order of memory deallocation before exit
+*
+* Revision 6.30  2002/08/05 21:54:02  dondosha
+* Added an #ifdef for QBLAST related stuff
+*
+* Revision 6.29  2002/06/18 22:18:31  dondosha
+* Typo correction
+*
+* Revision 6.28  2002/05/09 15:38:53  dondosha
+* Call BLASTOptionNewEx instead of BLASTOptionNew, so megablast defaults are set in a central place
+*
+* Revision 6.27  2002/05/07 14:53:56  dondosha
+* Copying bioseq was wrong - loses protein link for CDS translation; need only to pack the sequence itself
+*
+* Revision 6.26  2002/05/02 22:40:18  dondosha
+* Copy bioseqs if retrieved from ID1, removing non-residues from sequence
+*
+* Revision 6.25  2002/04/24 19:24:17  dondosha
+* Use QBlast API to retrieve sequences when RID is provided in the URL
+*
+* Revision 6.24  2002/03/19 23:31:06  dondosha
+* Do not increment options->wordsize by 4 for megablast any more
+*
+* Revision 6.23  2002/03/18 18:08:52  dondosha
+* 1. Cleaned up code differentiating between NCBI and 'standalone' versions
+* 2. Added DBLEN URL parameter to specify effective database length
+* 3. Added RID URL parameter to allow fetching sequences from BLAST Queue
+*
+* Revision 6.22  2002/01/09 23:26:57  dondosha
+* Change effective 12/27: get nr database size possibly using alias file
+*
+* Revision 6.21  2001/10/03 19:39:11  dondosha
+* Tiny correction in formatting of minus strand alignments
+*
+* Revision 6.20  2001/07/31 16:47:39  dondosha
+* Function FastaCheckDna made public for use in Web BLAST
+*
+* Revision 6.19  2001/07/27 16:06:42  dondosha
+* Roll back use of fake subject id, instead use SeqIdFindBest function
+*
+* Revision 6.18  2001/07/25 21:33:29  dondosha
+* Use fake subject Bioseq
+*
+* Revision 6.17  2001/07/23 20:22:02  dondosha
+* Corrected score data computation when query is masked
+*
+* Revision 6.16  2001/03/14 16:43:11  dondosha
+* Minor correction
+*
+* Revision 6.15  2001/03/02 20:48:55  dondosha
+* Cosmetic changes suggested by Roma Tatusov
+*
+* Revision 6.14  2001/02/26 21:32:09  dondosha
+* Do not remove non-alphanumeric characters from sequence in FastaCheckDna
+*
+* Revision 6.13  2001/02/16 20:21:01  dondosha
+* 1. Added a strand option menu
+* 2. Fixed bug in sequence id manipulation
+*
+* Revision 6.12  2001/01/09 21:01:20  dondosha
+* For megablast, subtract 4 from wordsize when displaying next page
+*
+* Revision 6.11  2001/01/04 18:28:28  dondosha
+* For tblastx, split seqalign into a linked list of seqaligns
+*
+* Revision 6.10  2000/12/21 15:57:32  dondosha
+* Test chptr for being NULL
+*
+* Revision 6.9  2000/12/07 17:58:04  dondosha
+* Enabled Mega BLAST extension choice for blastn program
+*
+* Revision 6.8  2000/11/22 19:35:11  dondosha
+* Minor fixes of purify errors and memory leaks
+*
+* Revision 6.7  2000/11/16 23:27:50  dondosha
+* Minor corrections from 11/07/2000
+*
+* Revision 6.6  2000/11/03 22:20:42  shavirin
+* Added return value from Main() function.
+*
+* Revision 6.5  2000/11/03 20:46:41  dondosha
+* A few bug fixes
+*
+* Revision 6.4  2000/11/03 16:39:17  shavirin
+* Added alternative formating for Standalone WWW Blast server.
+*
+* Revision 6.3  2000/11/02 21:45:41  dondosha
+* Removed printing content from code - should be done in the cgi script
+*
+* Revision 6.2  2000/11/02 20:51:00  dondosha
+* Significant clean up of the code
+*
+* Revision 6.1  2000/10/31 19:37:31  dondosha
+* Changed revision to 6.1
+*
+* Revision 1.4  2000/10/31 19:33:49  dondosha
+* Changed gif images paths to current directory
+*
+* Revision 1.2  2000/10/23 21:22:31  dondosha
+* Turned on CVS logging
+*
+* Revision 6.1
+* Source code for the Blast 2 Sequences Web page
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <tofasta.h>
+#include <wwwblast.h>
+#include <id1arch.h>
+/* For rlimit stuff. */
+#if defined(OS_UNIX)
+#include <sys/resource.h>
+#endif
+#include <signal.h>
+#include <stdarg.h>
+#ifndef BL2SEQ_STANDALONE
+#include <poll.h>
+#endif
+#include <time.h>
+
+#include <blastpat.h>
+#ifndef BL2SEQ_STANDALONE
+#include <objBlobj.h>
+#include <qblastnet.h>
+#endif
+
+#define MY_BLOSUM62 0
+#define MY_PAM30 1
+#define MY_PAM70 2
+#define MY_PAM250 3
+#define MY_BLOSUM90 4
+#define MY_BLOSUM50 5
+
+#define NR_SIZE_NA 2385885539
+#define NR_SIZE_AA 181542687
+
+typedef struct prym{
+	Int2		len;
+	Int2		color;
+	CharPtr 	sym;
+	Boolean		noleft, noright;
+} Prym, PNTR PrymPtr;
+
+
+static void JavaScriptFun()
+{
+   printf("<SCRIPT LANGUAGE=\"Javascript\">\n");
+   
+   printf("<!-- HIDE\n");
+   printf("function chan(a)\n");
+   printf("{\n");
+   printf("	if (a.value == 'off') {\n");
+   printf("		document.bl2.gopen.value=11;\n");
+   printf("		document.bl2.gext.value=1;\n");
+   printf("		document.bl2.match.value=\"\";\n");
+   printf("		document.bl2.msmatch.value=\"\";\n");
+   printf("		a.value = 'on';\n");
+   printf("	} else {\n");
+   printf("		document.bl2.gopen.value=5;\n");
+   printf("		document.bl2.gext.value=2;\n");
+   printf("		document.bl2.match.value=\"1\";\n");
+   printf("		document.bl2.msmatch.value=\"-2\";\n");
+   printf("		a.value = 'off';\n");
+   printf("	}\n");
+   printf("}\n");
+   
+   printf("function chan_prog(a)\n");
+   printf("{\n");
+   printf("	if (a.selectedIndex == 0) {\n");
+   printf("		document.bl2.gopen.value = 5;\n");
+   printf("		document.bl2.gext.value = 2;\n");
+   printf("		document.bl2.match.value=1;\n");
+   printf("		document.bl2.msmatch.value=\"-2\";\n");
+   printf("		document.bl2.word.value=\"11\";\n");
+   printf("             document.bl2.matrix.options.length = 1;\n");
+   printf("             document.bl2.matrix.options[0] = null;\n");
+   printf("             document.bl2.matrix.options[0] = new Option('Not Applicable');\n");
+   printf("             document.bl2.matrix.options[0].text='Not Applicable';\n");
+   printf("             document.bl2.matrix.options[0].value=-1;\n");
+   printf("             document.bl2.strand.options.length = 4;\n");
+   printf("             document.bl2.strand.options[0] = null;\n");
+   printf("             document.bl2.strand.options[0] = new Option('Both strands');\n");
+   printf("             document.bl2.strand.options[0].text='Both strands';\n");
+   printf("             document.bl2.strand.options[0].value=3;\n");
+   printf("             document.bl2.strand.options[1].text='Top strand';\n");
+   printf("             document.bl2.strand.options[1].value=1;\n");
+   printf("             document.bl2.strand.options[2].text='Reverse strand';\n");
+   printf("             document.bl2.strand.options[2].value=2;\n");
+   printf("	} else if (a.selectedIndex >= 1) {\n");
+   printf("             document.bl2.matrix.options.length = 7;\n");
+   printf("             document.bl2.matrix.options[0] = null;\n");
+   printf("             document.bl2.matrix.options[0] = new Option('BLOSUM62');\n");
+   printf("             document.bl2.matrix.options[0].selected = true;\n");
+   printf("             document.bl2.matrix.options[0].text='BLOSUM62';\n");
+   printf("             document.bl2.matrix.options[0].value=0;\n");
+   printf("             document.bl2.matrix.options[1].text='PAM30';\n");
+   printf("             document.bl2.matrix.options[1].value=1;\n");
+   printf("             document.bl2.matrix.options[2].text='PAM70';\n");
+   printf("             document.bl2.matrix.options[2].value=2;\n");
+   printf("             document.bl2.matrix.options[3].text='PAM250';\n");
+   printf("             document.bl2.matrix.options[3].value=3;\n");
+   printf("             document.bl2.matrix.options[4].text='BLOSUM90';\n");
+   printf("             document.bl2.matrix.options[4].value=4;\n");
+   printf("             document.bl2.matrix.options[5].text='BLOSUM50';\n");
+   printf("             document.bl2.matrix.options[5].value=5;\n");
+   printf("		document.bl2.word.value=\"3\";\n");
+   printf("		if (document.bl2.matrix.selectedIndex == 1) {\n");
+   printf("			document.bl2.gopen.value = 9;\n");
+   printf("			document.bl2.gext.value = 1;\n");
+   printf("		} else if (document.bl2.matrix.selectedIndex == 2) {\n");
+   printf("			document.bl2.gopen.value = 10;\n");
+   printf("			document.bl2.gext.value = 1;\n");
+   printf("		} else if (document.bl2.matrix.selectedIndex == 3) {\n");
+   printf("			document.bl2.gopen.value = 14;\n");
+   printf("			document.bl2.gext.value = 2;\n");
+   printf("		} else if (document.bl2.matrix.selectedIndex == 4) {\n");
+   printf("			document.bl2.gopen.value =10;\n");
+   printf("			document.bl2.gext.value = 1;\n");
+   printf("		} else if (document.bl2.matrix.selectedIndex == 5) {\n");
+   printf("			document.bl2.gopen.value = 13;\n");
+   printf("			document.bl2.gext.value = 2;\n");
+   printf("		} else {\n");
+   printf("			document.bl2.gopen.value = 11;\n");
+   printf("			document.bl2.gext.value = 1;\n");
+   printf("		}\n"); 
+   printf("		document.bl2.match.value=\"\";\n");
+   printf("		document.bl2.msmatch.value=\"\";\n");
+   printf("		document.bl2.megablast.checked = 0;\n");
+   printf("             document.bl2.strand.options.length = 1;\n");
+   printf("             document.bl2.strand.options[0] = null;\n");
+   printf("             document.bl2.strand.options[0] = new Option('Not Applicable');\n");
+   printf("             document.bl2.strand.options[0].selected = true;\n");
+   printf("             document.bl2.strand.options[0].text='Not Applicable';\n");
+   printf("             document.bl2.strand.options[0].value=0;\n");
+   printf("	}\n");
+   printf("}\n");
+   
+   printf("function update_mtrx(a)\n");
+   printf("{\n");
+   printf("	if (document.bl2.program.selectedIndex == 0) {\n");
+   printf("		return;\n");
+   printf("	}\n");
+   printf("     document.bl2.word.value = 3;\n");
+   printf("	if (a.selectedIndex == 0) {\n");
+   printf("		document.bl2.gopen.value = 11;\n");
+   printf("		document.bl2.gext.value = 1;\n");
+   printf("	} else if (a.selectedIndex == 1) {\n");
+   printf("		document.bl2.gopen.value = 9;\n");
+   printf("		document.bl2.gext.value = 1;\n");
+   printf("	} else if (a.selectedIndex == 2) {\n");
+   printf("		document.bl2.gopen.value = 10;\n");
+   printf("		document.bl2.gext.value = 1;\n");
+   printf("	} else if (a.selectedIndex == 3) {\n");
+   printf("		document.bl2.gopen.value = 14;\n");
+   printf("		document.bl2.gext.value = 2;\n");
+   printf("	} else if (a.selectedIndex == 4) {\n");
+   printf("		document.bl2.gopen.value = 10;\n");
+   printf("		document.bl2.gext.value = 1;\n");
+   printf("	} else if (a.selectedIndex == 5) {\n");
+   printf("		document.bl2.gopen.value = 13;\n");
+   printf("		document.bl2.gext.value = 2;\n");
+   printf("	}\n");
+   printf("}\n");
+
+   /* Function clear_sequence() */
+   printf("function clear_sequence() {\n");
+   printf("    document.bl2.seqfile1.value=''\n");
+   printf("    document.bl2.seqfile2.value=''\n");
+   printf("    document.bl2.sseq.value=''\n");
+   printf("    document.bl2.seq.value=''\n");
+   printf("    document.bl2.one.value=''\n");
+   printf("    document.bl2.two.value=''\n");
+   printf("    document.bl2.to.value=''\n");
+   printf("    document.bl2.tto.value=''\n");
+   printf("    document.bl2.from.value=''\n");
+   printf("    document.bl2.ffrom.value=''\n");
+   printf("    document.bl2.seq.focus()\n");
+   printf("}\n");
+   
+   /* Function megablast_update(a) */
+   printf("function megablast_update(a)\n");
+   printf("{\n");
+   printf("	if (a.checked == 0) {\n");
+   printf("         document.bl2.word.value = 11;\n");
+   printf("         document.bl2.gopen.value = 5;\n");
+   printf("         document.bl2.gext.value = 2;\n");
+   printf("	} else {\n");
+   printf("         if (document.bl2.program.selectedIndex != 0) {\n");
+   printf("            document.bl2.program.selectedIndex = 0;\n");     
+   printf("            chan_prog(document.bl2.program);\n");
+   printf("         }\n");
+   printf("         document.bl2.word.value = 28;\n");
+   printf("         document.bl2.gopen.value = \"\";\n");
+   printf("         document.bl2.gext.value = \"\";\n");
+   printf("     }\n");
+   printf("}\n");
+
+   printf("// -->\n");
+    
+   printf("</SCRIPT>\n");
+   return;
+}
+
+static SeqAnnotPtr tie_next_annot(SeqAnnotPtr head, SeqAnnotPtr next)
+{
+   SeqAnnotPtr v;
+   
+   if (head == NULL) {
+      return next;
+   }
+   for (v = head; v->next != NULL; v = v->next) {
+      v = v;
+   }
+   v->next = next;
+   return head;
+}
+
+static void AbortPage(CharPtr mess)
+{
+   printf("<TITLE>ERROR</TITLE>\n");
+   printf("<h2>\n");
+   printf("<img src='images/confused.gif' align=middle>\n");
+   printf("%s</h2>\n", mess);
+   exit(1);
+}
+
+#ifndef BL2SEQ_STANDALONE/* No logging for the standalone WWW Server version */
+typedef struct LogInfo {
+   CharPtr filename;
+   time_t time_start;
+   clock_t cpu_time;
+   Int4 pid;
+   CharPtr program;
+   Int4 q_length;
+   Int4 s_length;
+   CharPtr user_IP;
+   Int4 size;
+} LogInfo;
+
+static LogInfo loginfo;
+
+static void LogInfoFree()
+{
+   MemFree(loginfo.filename);
+   MemFree(loginfo.program);
+   MemFree(loginfo.user_IP);
+}
+
+#endif
+
+#ifndef BL2SEQ_STANDALONE/* No logging for the standalone WWW Server version */
+void logmsg(int status)
+{
+    FILE *logfp;
+
+    if ((logfp = FileOpen(loginfo.filename, "a")) != NULL) {
+       if (loginfo.time_start == 0) {
+          loginfo.cpu_time = clock();
+          loginfo.time_start = time(NULL);
+          fprintf(logfp, "%ld|%d|%s|%ld|%ld|%s|start\n", loginfo.time_start, 
+                  loginfo.pid, loginfo.program, loginfo.q_length,
+                  loginfo.s_length, loginfo.user_IP);
+       } else {
+          struct tm tt;
+          char tmstamp[128];
+          memcpy(&tt, localtime(&loginfo.time_start), sizeof(tt));
+          strftime(tmstamp, sizeof(tmstamp), "%Y-%m-%d %T", &tt);
+          loginfo.cpu_time = (clock() - loginfo.cpu_time) / CLOCKS_PER_SEC;
+ 
+          fprintf(logfp, "%ld|%s|%ld|%d|%s|%ld|%ld|%s|done|%d|%ld|%ld\n", 
+                  loginfo.time_start, tmstamp, loginfo.cpu_time, loginfo.pid, 
+                  loginfo.program, loginfo.q_length, loginfo.s_length, 
+                  loginfo.user_IP, status, time(NULL) - loginfo.time_start, 
+                  loginfo.size);
+       }
+       FileClose(logfp);
+    }
+}
+#endif
+
+/* Controls the state of the signal handling thread */
+static Boolean run_status;
+/* Flag to indicate which signals were received */ 
+static Uint8 sigflag = 0;
+/* set of signal masks */
+static Uint8 sigmask[64];
+
+#define WBLAST2_SEARCH 0
+#define WBLAST2_FORMAT 1
+#define WBLAST2_DONE   2
+
+/** precompute individual sigmasks */
+void PrepareSigmask(void)
+{
+   int ii;
+   for( ii = 0; ii < 64; ii++ ) {
+      sigmask[ii] = 1 << ii;
+   }
+}
+
+/** */
+static int GetSignal()
+{
+   int ii;
+   for( ii = 0; ii < 64; ii++ ) {
+      if( sigflag & sigmask[ii] ) {
+         break;
+      }
+   }
+   
+   return ii;
+}
+
+/** set signal flag */
+static void sighandler(int sig)
+{
+   sigflag |= sigmask[sig];
+}
+
+static void	Blast2SeqMainPage(CharPtr warning, CharPtr seq1, CharPtr seq2, CharPtr one, CharPtr two, ValNodePtr error, Boolean is_prot, BLAST_OptionsBlkPtr options, Int2 mtrx, Int4 from, Int4 to, Int4 ffrom, Int4 tto, Int2 filter, Int2 pagecount) {
+/*****************************************************************
+	0 - no sequences
+	1 - nucleotide sequences in protein alignment
+	2 - non-nucleotide sequences in nucleotide alignment
+	4 - BLAST Options error mesg handling
+	5 - invalid location
+	6 - No alignment found
+*****************************************************************/
+	ValNodePtr vnp;
+	BlastErrorMsgPtr error_msg;
+	Int4Ptr dgopen=NULL, dgext=NULL;
+        Uint1 prog_number;
+
+        if (options)
+           prog_number = BlastGetProgramNumber(options->program_name);
+        else 
+           prog_number = 1;
+
+	switch (mtrx) {
+        case MY_PAM30:
+           BlastKarlinGetMatrixValues("PAM30", 
+                                      &dgopen, &dgext, NULL, NULL, NULL, NULL);
+           break;
+        case MY_PAM70:
+           BlastKarlinGetMatrixValues("MY_PAM70", 
+                                      &dgopen, &dgext, NULL, NULL, NULL, NULL);
+           break;
+        case MY_PAM250:
+           BlastKarlinGetMatrixValues("MY_PAM250", 
+                                      &dgopen, &dgext, NULL, NULL, NULL, NULL);
+           break;
+        case MY_BLOSUM90:
+           BlastKarlinGetMatrixValues("MY_BLOSUM90", 
+                                      &dgopen, &dgext, NULL, NULL, NULL, NULL);
+           break;
+        case MY_BLOSUM50:
+           BlastKarlinGetMatrixValues("MY_BLOSUM50", 
+                                      &dgopen, &dgext, NULL, NULL, NULL, NULL);
+           break;
+        case MY_BLOSUM62:
+        default:
+           BlastKarlinGetMatrixValues("MY_BLOSUM62", 
+                                      &dgopen, &dgext, NULL, NULL, NULL, NULL);
+           break;
+	}
+
+	printf("<html>\n");
+	printf("<head>\n");
+	printf("<title>Blast 2 Sequences</title>\n");
+        printf("<META NAME=\"keywords\" CONTENT=\"NCBI, BLAST, ORF, Bioinformatics\">\n");
+#ifndef BL2SEQ_STANDALONE
+        printf("<link rel=\"stylesheet\" href=\"http://www.ncbi.nlm.nih.gov/ncbi.css\">\n");
+#endif
+	JavaScriptFun();
+	printf("</HEAD>\n");
+
+#ifndef BL2SEQ_STANDALONE
+	printf("<body bgcolor=\"#f0f0fe\">\n");
+        if (options) {
+           printf("<table border=0 width=600 cellspacing=0 cellpadding=0>\n");
+           printf("<tr valign=center> \n");
+           printf("<td width=140><A HREF=\"http://www.ncbi.nlm.nih.gov\"><img src=\"http://www.ncbi.nlm.nih.gov/corehtml/left.GIF\" width=130 height=45 border=0 ALT=\"NCBI logo\"></A></td>\n");
+           printf("<td width=460 ><h1>Blast 2 Sequences</h1></td>\n");
+           printf("</tr>\n");
+           printf("</table>\n");
+           
+           printf("<!--  the quicklinks bar--> \n");
+           printf("<table border=0 width=600 cellspacing=0 cellpadding=1 bgcolor=#003366>\n");
+           printf("<tr align=\"center\">\n");
+           printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed\" class=\"BAR\"><FONT COLOR=#FFFFFF>PubMed</FONT></a></td>\n");
+           printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/Entrez/\" class=\"BAR\"><FONT COLOR=#FFFFFF>Entrez</FONT></a></td>\n");
+           printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/blast/\" class=\"BAR\"><FONT COLOR=#FFFFFF>BLAST</FONT></a></td>\n");
+           printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/omim/\" class=\"BAR\"><FONT COLOR=#FFFFFF>OMIM</FONT></a></td>\n");
+           printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html\" class=\"BAR\"><FONT COLOR=#FFFFFF>Taxonomy</FONT></a></td>\n");
+           printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/Structure/\" class=\"BAR\"><FONT COLOR=#FFFFFF>Structure</FONT></a></td>\n");
+           printf("</tr></table>\n");
+        } else {
+           printf("<CENTER><TABLE CELLSPACING=2 CELLPADDING=2 WIDTH=100%%>\n");
+           printf("<TR ALIGN=CENTER BaGCOLOR=#8dc7cc BGCOLOR=#0000ff><TD><B><I>\n");
+           printf("<A HREF=http://www.ncbi.nlm.nih.gov/><font color=#ffffff>NCBI</font></A></I></B></TD>\n");
+           printf("<TD><B><I>\n");
+           printf("<A HREF=http://www.ncbi.nlm.nih.gov/Entrez><font color=#ffffff>Entrez</font></A>\n");
+           printf("</I></B></TD>\n");
+           printf("<TD><B><I><A HREF=bl2.html><font color=#ffffff>BLAST 2 sequences</font></A></I></B></TD>\n");
+           printf("<TD><B><I><A HREF=http://www.ncbi.nlm.nih.gov/blast><font color=#ffffff>BLAST</font></A></I></B></TD>\n");
+           printf("<TD><B><I><A HREF=bl2_seg.html><font color=#ffffff>Example</font></A></I></B></TD>\n");
+           printf("<TD><B><I>\n");
+           printf("<A HREF=http://www.ncbi.nlm.nih.gov/blast/blast_help.html><font color=#ffffff>Help</font></A>\n");
+           printf("</I></B></TD></TR></TABLE></CENTER>\n");
+        }
+        printf("<H2><CENTER><font color=#0000ff> BLAST 2 SEQUENCES</font></H2></CENTER>\n");
+        printf("<FORM NAME=\"bl2\" method=\"Post\" action=\"wblast2.cgi?%d\" enctype=\"multipart/form-data\">\n", pagecount);
+#else /* defined BL2SEQ_STANDALONE */
+    printf("<BODY BGCOLOR=\"#F0F0FE\" LINK=\"#0000FF\" "
+           "VLINK=\"#660099\" ALINK=\"#660099\">\n");
+    printf("<A HREF=\"blast_form.map\">"
+           "<IMG SRC=\"images/bl2seq.gif\" BORDER=0 ISMAP></A>\n");
+    printf("<FORM NAME=\"bl2\" method=\"POST\" "
+#ifdef NCBI_ENTREZ_CLIENT
+           "action=\"wblast2_cs.cgi?%d\" "
+#else
+           "action=\"wblast2.cgi?%d\" "
+#endif
+           "enctype=\"multipart/form-data\">\n", pagecount);
+#endif
+        if (warning)
+           printf("<h3><font color=#EE0000>WARNING:</font><font color=#0000EE> %s</font></h3>", warning);
+        else {
+           for (vnp=error; vnp; vnp=vnp->next) {
+              error_msg = vnp->data.ptrvalue;
+              printf("<h3><font color=#EE0000>WARNING:</font><font color=#0000EE> %s</font></h3>", error_msg->msg);
+           }
+        }
+        if (!options) {
+           printf("This tool produces the alignment of two given sequences using "
+#ifndef BL2SEQ_STANDALONE
+"<A HREF=http://www.ncbi.nlm.nih.gov/blast/newblast.html TARGET=one>BLAST</A> engine for local alignment. <BR>The stand-alone executable for blasting two sequences (bl2seq) can be retrieved from <A HREF=ftp://ncbi.nlm.nih.gov/blast/executables> NCBI ftp site</A><br><b><A HREF=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10339815&dopt=Abstract>Reference:</A></b> Tatiana A. Tatusova, Thomas L. Madden (1999), \"Blast 2 sequences - a new tool for comparing protein and nucleotide sequences\", FEMS Microbiol Lett. 174:247-250 \
+<br><BR>"
+#else
+"BLAST<BR>engine for local alignment.<P>\n"
+#endif
+                  );
+        }
+#ifndef BL2SEQ_STANDALONE
+        printf("<A HREF=http://www.ncbi.nlm.nih.gov/blast/blast_program.html TARGET=one>Program</A>\n");
+#else
+        printf("<A HREF=\"docs/blast_program.html\">Program</A>\n");
+#endif
+        printf("<select name=\"program\" onChange=\"chan_prog(this)\">\n");
+        printf("<option%s> blastn\n", (prog_number == blast_type_blastn) ? " SELECTED" : "");
+        printf("<option%s> blastp\n", (prog_number == blast_type_blastp) ? " SELECTED" : "");
+        printf("<option%s> tblastn\n", (prog_number == blast_type_tblastn) ? " SELECTED" : "");
+        printf("<option%s> blastx\n", (prog_number == blast_type_blastx) ? " SELECTED" : "");
+        printf("<option%s> tblastx\n", (prog_number == blast_type_tblastx) ? " SELECTED" : "");
+        printf("</select>\n");
+#ifndef BL2SEQ_STANDALONE
+        printf("<A HREF=http://www.ncbi.nlm.nih.gov/blast/options.html#matrix TARGET=one>Matrix</A>\n");
+#else
+        printf("<A HREF=docs/options.html#matrix>Matrix</A>\n");
+#endif
+        printf("<select name=\"matrix\" onChange=\"update_mtrx(this)\">\n");
+        if (prog_number != blast_type_blastn) {
+           printf("<option value=0>BLOSUM62\n");
+           printf("<option value=1%s>PAM30\n", (mtrx == 1) ? " SELECTED" : "");
+           printf("<option value=2%s>PAM70\n", (mtrx == 2) ? " SELECTED" : "");
+           printf("<option value=3%s>PAM250\n", (mtrx == 3) ? " SELECTED" : "");
+           printf("<option value=4%s>BLOSUM90\n", (mtrx == 4) ? " SELECTED" : "");
+           printf("<option value=5%s>BLOSUM50\n", (mtrx == 5) ? " SELECTED" : "");
+        } else 
+           printf("<option> Not Applicable\n");
+        printf("</select>\n");
+
+        printf("<HR>\n");
+        
+        /* -------------------------------------------------- */
+        printf("Parameters used in <A HREF="
+#ifndef BL2SEQ_STANDALONE   
+               "http://www.ncbi.nlm.nih.gov/blast/full_options.html#blastn TARGET=one>"
+#else
+               "docs/full_options.html#blastn> "
+#endif
+               "BLASTN </A>program only:<BR>\n");
+        if (options) {
+            printf("<strong>Match:</strong><INPUT type=text size=8 name=\"match\"%s>", 
+                   (is_prot == FALSE) ? " value=1" : "");
+            printf("<strong>Mismatch:</strong><INPUT type=text size=8 name=\"msmatch\"%s>",
+                   (is_prot == FALSE) ? " value=-2" : "");
+            printf("<BR>\n");
+            printf("Open gap\n");
+            printf("<INPUT type=text size=4 name=\"gopen\" value=%d>\n", 
+                   options->gap_open);
+            printf("and extension gap\n");
+            printf("<INPUT type=text size=4 name=\"gext\" value=%d> penalties<BR>\n", options->gap_extend);
+            printf("gap x_dropoff\n");
+            printf("<INPUT type=text size=4 name=\"dropoff\" value=%d>\n", options->gap_x_dropoff);
+            printf("<A HREF=http://www.ncbi.nlm.nih.gov/blast/newoptions.html#expect>expect</A>\n");
+            printf("<INPUT type=text size=4 name=\"expect\" value=%f>\n", options->expect_value);
+            printf(" word size\n");
+            printf("<INPUT type=text size=4 name=\"word\" value=%d>\n",
+                   options->wordsize);
+        } else {
+            printf("<strong>Reward for a match:</strong><INPUT type=text size=8 name=\"match\"%s>", 
+                   (is_prot == FALSE) ? " value=1" : "");
+            printf("<strong>Penalty for a mismatch:</strong><INPUT type=text size=8 name=\"msmatch\"%s>",
+                   (is_prot == FALSE) ? " value=-2" : "");
+            printf("<BR><BR>\n");
+            printf("<INPUT type=checkbox NAME=megablast onClick=\"megablast_update(this)\"> Use <a href="
+#ifndef BL2SEQ_STANDALONE
+                   "http://www.ncbi.nlm.nih.gov/blast/megablast.html"
+#else
+                   "docs/megablast_readme.html"
+#endif
+                   ">Mega BLAST</a>&nbsp;&nbsp;&nbsp;");
+            printf("Strand option <select name=\"strand\">\n");
+            printf("<option value=3 SELECTED> Both strands\n");
+            printf("<option value=1> Forward strand\n");
+            printf("<option value=2> Reverse strand\n");
+            printf("</select><HR>\n");
+
+            printf("Open gap\n");
+            printf("<INPUT type=text size=4 name=\"gopen\" value=5>\n");
+            printf("and extension gap\n");
+            printf("<INPUT type=text size=4 name=\"gext\" value=2> penalties<BR>\n");
+            printf("gap x_dropoff\n");
+            printf("<INPUT type=text size=4 name=\"dropoff\" value=50>\n");
+            printf("<A HREF=http://www.ncbi.nlm.nih.gov/blast/newoptions.html#expect>expect</A>\n");
+            printf("<INPUT type=text size=4 name=\"expect\" value=10.0>\n");
+            printf(" word size\n");
+            printf("<INPUT type=text size=4 name=\"word\" value=11>\n");
+        }
+        printf("<a href="
+#ifndef BL2SEQ_STANDALONE
+               "http://www.ncbi.nlm.nih.gov/blast"
+#else
+               "docs"
+#endif
+               "/newoptions.html#filter>Filter</a>\n");
+        printf("<INPUT TYPE=checkbox NAME=Filter VALUE=%d", filter);
+        if (filter == 1) {
+           printf(" CHECKED>\n");
+        } else {
+           printf(">\n");
+        }
+        printf("<INPUT TYPE=\"submit\" VALUE=\"Align\">\n");
+        if (options)
+           printf("<INPUT TYPE=\"reset\" VALUE=\"Clear Input\">\n");
+        
+        printf("<HR>\n");
+#ifdef NCBI_ENTREZ_CLIENT
+        printf("<font color=ff0000>Sequence 1</font> Enter accession or GI <INPUT type=text size=8 name=\"one\"");
+        if (one) {
+           printf("value=%s>\n", one);
+        } else {
+           printf(">\n");
+        }
+        printf("or download from file <INPUT type=file name=\"seqfile1\">");
+#else
+        printf("Download sequence from file <INPUT type=file name=\"seqfile1\">");
+#endif
+
+        printf("<BR>or sequence in FASTA format <font color=ff0000>from:<INPUT type=text size=8 name=\"from\" value=%d>to:<INPUT type=text size=8 name=\"to\" value=%d></font><BR>\n", from, to);
+        
+        printf("<textarea name=\"seq\" rows=6 cols=60>");
+        if (seq1) {
+           if (*seq1 == '>') {
+              printf("&gt;");
+              seq1++;
+           }
+           printf("%s</textarea>\n", seq1);
+        } else {
+           printf("</textarea>\n");
+        }
+        printf("<BR>\n");
+#ifdef NCBI_ENTREZ_CLIENT
+        printf("<font color=ff0000>Sequence 2</font> Enter accession or GI <INPUT type=text size=8 name=\"two\"");
+        if (two) {
+           printf("value=%s>\n", two);
+        } else {
+           printf(">\n");
+        }
+        printf("or download from file <INPUT type=file name=\"seqfile2\">");
+#else
+        printf("Download sequence from file <INPUT type=file name=\"seqfile2\">");
+#endif
+
+        printf("<BR>or sequence in FASTA format <font color=ff0000>from:<INPUT type=text size=8 name=\"ffrom\" value=%d>to:<INPUT type=text size=8 name=\"tto\" value=%d></font><BR>\n", ffrom, tto);
+        printf("<textarea name=\"sseq\" rows=6 cols=60>");
+        if (seq2) {
+           if (*seq2 == '>') {
+              printf("&gt;");
+              seq2++;
+           }
+           printf("%s</textarea>\n", seq2);
+        } else {
+           printf("</textarea>\n");
+        }
+
+        printf("<BR>\n");
+        printf("<INPUT TYPE=\"submit\" VALUE=\"Align\">\n");
+        printf("<INPUT TYPE=\"reset\" VALUE=\"Clear Input\">\n");
+        printf("<INPUT TYPE=hidden name=\"page\" value=\"%d\">\n", pagecount+1);
+        if (options)
+            printf("<INPUT TYPE=hidden name=\"program\" value=\"%s\">\n",
+                   options->program_name);
+        else
+            printf("<INPUT TYPE=hidden name=\"program\" value=\"blastn\">\n");
+	
+        printf("</form>\n");
+        printf("<HR>\n");
+        printf("<ADDRESS> Comments and suggestions to");
+        printf(" <A HREF=\"mailto:blast-help@ncbi.nlm.nih.gov\">blast-help@ncbi.nlm.nih.gov</A>\n");
+        printf("<BR>\n");
+        printf("</body>\n");
+        printf("</html>\n");
+        fflush(stdout);
+
+        options = BLASTOptionDelete(options);
+
+        exit (0);
+}
+
+static void CreateJavaHeadHTML(BioseqPtr query_bsp, BioseqPtr subject_bsp, Int4 from, Int4 to, Int4 ffrom, Int4 tto, Int4 len1, Int4 len2, CharPtr progname)
+{
+	static Char tmp[128];
+		
+	printf("<HTML>\n");
+	printf("<head>\n");
+	printf("<title>Blast Result</title>\n\n");
+        printf("<META NAME=\"keywords\" CONTENT=\"NCBI, BLAST, ORF, Bioinformatics\">\n");
+#ifndef BL2SEQ_STANDALONE
+        printf("<link rel=\"stylesheet\" href=\"http://www.ncbi.nlm.nih.gov/ncbi.css\">\n");
+#endif
+	JavaScriptFun();
+	printf("</head>\n");
+#ifndef BL2SEQ_STANDALONE
+	printf("<BODY bgcolor=\"#f0f0fe\">\n");
+        printf("<table border=0 width=600 cellspacing=0 cellpadding=0>\n");
+        printf("<tr valign=center> \n");
+        printf("<td width=140><A HREF=\"http://www.ncbi.nlm.nih.gov\"><img src=\"http://www.ncbi.nlm.nih.gov/corehtml/left.GIF\" width=130 height=45 border=0 ALT=\"NCBI logo\"></A></td>\n");
+        printf("<td width=460 ><h1>Blast 2 Sequences results</h1></td>\n");
+        printf("</tr>\n");
+        printf("</table>\n");
+        printf("<!--  the quicklinks bar--> \n");
+        printf("<table border=0 width=600 cellspacing=0 cellpadding=1 bgcolor=#003366>\n");
+        printf("<tr align=\"center\">\n");
+        printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed\" class=\"BAR\"><FONT COLOR=#FFFFFF>PubMed</FONT></a></td>\n");
+        printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/Entrez/\" class=\"BAR\"><FONT COLOR=#FFFFFF>Entrez</FONT></a></td>\n");
+        printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/blast/\" class=\"BAR\"><FONT COLOR=#FFFFFF>BLAST</FONT></a></td>\n");
+        printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/omim/\" class=\"BAR\"><FONT COLOR=#FFFFFF>OMIM</FONT></a></td>\n");
+        printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html\" class=\"BAR\"><FONT COLOR=#FFFFFF>Taxonomy</FONT></a></td>\n");
+        printf("<td width=100><a href=\"http://www.ncbi.nlm.nih.gov/Structure/\" class=\"BAR\"><FONT COLOR=#FFFFFF>Structure</FONT></a></td>\n");
+        printf("</tr></TABLE><p>\n");
+#else
+    printf("<BODY BGCOLOR=\"#F0F0FE\" LINK=\"#0000FF\" "
+           "VLINK=\"#660099\" ALINK=\"#660099\">\n");
+    
+    printf("<A HREF=\"blast_form.map\">"
+           "<IMG SRC=\"images/bl2seq.gif\" BORDER=0 ISMAP></A>\n<P>");    
+#endif        
+        init_buff();
+   	sprintf(tmp, "BLAST 2 sequences results version %s", progname);
+        BlastPrintVersionInfo(tmp, TRUE, stdout);
+	free_buff();
+
+	return;
+}
+
+ 
+static void CreateTailHTML()
+{
+    printf("<br>\n");
+    printf("</BODY>\n");
+    printf("</HTML>\n");
+}
+
+static int NumToGun1(int n)
+{
+    return (n < 10) ? n+'0' : (n < 36) ? n-10+'A' : n-36+'a';
+}
+
+static CharPtr NumToGun(int n)
+{
+    static Char str[4];
+    
+    str[0] = NumToGun1(n/62);
+    str[1] = NumToGun1(n%62);
+    return str;
+}
+
+static int get_int(CharPtr val)
+{
+	CharPtr ch=NULL;
+	
+	if (val != NULL) {
+		ch = val + 1;
+		while (isspace(*ch)) {
+			ch++;
+		}
+		if (*ch == '\0') {
+			return 0;
+		}
+		return (atoi(ch));
+	}
+	return 0;
+}
+static FloatHi get_double(CharPtr val)
+{
+	CharPtr ch=NULL;
+	
+	if (val != NULL) {
+		ch = val + 1;
+		while (isspace(*ch)) {
+			ch++;
+		}
+		if (*ch == '\0') {
+			return 0;
+		}
+		return (atof(ch));
+	}
+	return 0;
+}
+
+static CharPtr get_char(CharPtr val)
+{
+	CharPtr ch=NULL;
+	
+	if (val != NULL) {
+		ch = val + 1;
+		while (isspace(*ch)) {
+			ch++;
+		}
+		if (*ch == '\0') {
+			ch = NULL;
+		}
+	}
+	return ch;
+}
+
+static Boolean sum_for_DenseDiag(DenseDiagPtr ddp, AlignSumPtr asp)
+/* special for blast 2 sequences */
+{
+	SeqInt msi, tsi;
+	SeqLoc sl;
+	Int2 i;
+	Int4 x1, x2, y1, y2;
+	Uint1 m_res, t_res;
+	SeqPortPtr m_spp, t_spp;
+
+	if(ddp == NULL || asp == NULL)
+		return FALSE;
+	x1 = ddp->starts [0];
+	y1 = ddp->starts [1];
+	x2 = x1 + ddp->len - 1;
+	y2 = y1 + ddp->len - 1;
+	msi.id = ddp->id;
+	msi.from = x1;
+	msi.to = x2;
+	if(ddp->strands != NULL)
+		msi.strand = (ddp->strands == NULL) ? 0 : ddp->strands[0];
+	sl.choice = SEQLOC_INT;
+	sl.data.ptrvalue = &msi;
+	m_spp = SeqPortNewByLoc(&sl, 
+		(asp->is_aa) ? Seq_code_ncbieaa : Seq_code_iupacna);
+	
+	tsi.id = ddp->id;
+	tsi.from = y1;
+	tsi.to = y2;
+	if(ddp->strands != NULL)
+		tsi.strand = (ddp->strands == NULL) ? 0 : ddp->strands[1];
+	sl.choice = SEQLOC_INT;
+	sl.data.ptrvalue = &tsi;
+
+	t_spp = SeqPortNewByLoc(&sl, 
+		(asp->is_aa) ? Seq_code_ncbieaa : Seq_code_iupacna);
+
+	for(i = 0; i < ddp->len; ++i) {
+		m_res = SeqPortGetResidue(m_spp);
+		if (!IS_residue(m_res)) {
+			continue;
+		}
+		t_res = SeqPortGetResidue(t_spp);
+		if (!IS_residue(t_res)) {
+			continue;
+		}
+		if(m_res == t_res) {
+			++(asp->identical);
+		} else if(asp->matrix != NULL && asp->is_aa) {
+			if(asp->matrix[m_res][t_res] > 0)
+				++(asp->positive);
+		}
+	}
+
+        if (!asp->is_aa && ddp->strands) {
+           asp->m_strand = ddp->strands[0];
+           asp->t_strand = ddp->strands[1];
+        }
+	asp->totlen = ddp->len;
+
+	SeqPortFree(m_spp);
+	SeqPortFree(t_spp);
+	return TRUE;
+}
+
+static Boolean sum_for_DenseSeg(DenseSegPtr dsp, AlignSumPtr asp)
+{
+/* special for blast 2 sequences */
+	SeqInt msi, tsi;
+	SeqLoc sl;
+	Int2 i;
+	Int4 j, x1, x2, y1, y2;
+	Uint1 m_res, t_res;
+	SeqPortPtr m_spp, t_spp;
+
+	if(dsp == NULL || asp == NULL)
+		return FALSE;
+	for(i = 0; i < dsp->numseg; ++i) {
+		x1 = dsp->starts[2*i];
+		y1 = dsp->starts[2*i+1];
+		x2 = x1 + dsp->lens[i] -1;
+		y2 = y1 + dsp->lens[i] -1;
+		msi.id = dsp->ids;
+		msi.from = x1;
+		msi.to = x2;
+		msi.strand = (dsp->strands == NULL) ? 0 : dsp->strands[2*i];
+                if (x1 != -1) {
+                   sl.choice = SEQLOC_INT;
+                   sl.data.ptrvalue = &msi;
+                   m_spp = SeqPortNewByLoc(&sl, (asp->is_aa) ? Seq_code_ncbieaa
+                                           : Seq_code_iupacna);
+                } else 
+                   m_spp = NULL;
+		tsi.id = dsp->ids->next;
+		tsi.from = y1;
+		tsi.to = y2;
+		tsi.strand = (dsp->strands == NULL) ? 0 :
+                   dsp->strands[2*i+1];
+                if (y1 != -1) {
+                   sl.choice = SEQLOC_INT;
+                   sl.data.ptrvalue = &tsi;
+                   t_spp = SeqPortNewByLoc(&sl, (asp->is_aa) ? Seq_code_ncbieaa : Seq_code_iupacna);
+                } else 
+                   t_spp = NULL;
+		if (x1 == -1 || y1 == -1) {
+			asp->gaps += dsp->lens[i];
+		} else {
+			for(j = 0; j < dsp->lens[i]; ++j) {
+				m_res = SeqPortGetResidue(m_spp);
+				if (!IS_residue(m_res)) {
+					continue;
+				}
+				t_res = SeqPortGetResidue(t_spp);
+				if (!IS_residue(m_res)) {
+					continue;
+				}
+				if(m_res == t_res) {
+					++(asp->identical);
+				} else if(asp->matrix != NULL && asp->is_aa) {
+					if(asp->matrix[m_res][t_res] >0)
+						++(asp->positive);
+				}
+			}
+		}
+		asp->totlen += dsp->lens[i];
+                SeqPortFree(m_spp);
+                SeqPortFree(t_spp);
+	}
+        asp->m_strand = msi.strand;
+        asp->t_strand = tsi.strand;
+        
+	return TRUE;
+}
+
+/* static functions from txalign.c needed for SEG masking */
+static void MaskWithLowComplexity(ByteStorePtr bsp, SeqLocPtr maskloc, Uint1 mol)
+{
+	SeqLocPtr slp = NULL;
+	Int4 start, stop;
+	Uint1 res = 'N';
+	
+
+	if(mol == Seq_mol_aa)
+		res = 'X';
+
+	while(maskloc)
+	{
+		slp = NULL;
+ 		while((slp = SeqLocFindNext(maskloc, slp))!=NULL)
+		{
+			start = SeqLocStart(slp);
+			stop = SeqLocStop(slp);
+			BSSeek(bsp, start, SEEK_SET);
+			for(; start <=stop; ++start)
+                BSPutByte(bsp, (Int2)res);
+		}
+		maskloc = maskloc->next;
+	}
+}
+
+static ByteStorePtr create_byte_store_from_bsp (BioseqPtr bsp)
+{
+	SeqPortPtr spp;
+	Uint1 code;
+	ByteStorePtr b_store;
+	Uint1 residue;
+
+	if(bsp == NULL)
+		return NULL;
+	if(bsp->mol == Seq_mol_aa)
+		code = Seq_code_iupacaa;
+	else
+		code = Seq_code_iupacna;
+
+	spp = SeqPortNew(bsp, 0, bsp->length-1, Seq_strand_plus, code);
+	b_store = BSNew(bsp->length +1);
+	BSSeek(b_store, 0, SEEK_SET);
+	while((residue = SeqPortGetResidue(spp)) != SEQPORT_EOF)
+		BSPutByte(b_store, (Int2)residue);
+	SeqPortFree(spp);
+	return b_store;
+}
+
+static ValNodePtr CreateMaskByteStore (ValNodePtr mask_list)
+{
+	BioseqPtr bsp;
+	SeqLocPtr slp;
+	SeqIdPtr sip;
+	ValNodePtr list, curr;
+	ByteStorePtr b_store, c_store;
+	Uint1 mol;
+
+	list = NULL;
+	b_store = NULL;
+	while(mask_list)
+	{
+		curr = ValNodeNew(list);
+		curr->choice = mask_list->choice;
+		if(list == NULL)
+			list = curr;
+		slp = mask_list->data.ptrvalue;
+		if(slp != NULL)
+		{
+			if(b_store == NULL)
+			{
+				sip = SeqLocId(slp);
+				if(sip != NULL)
+				{
+					bsp = BioseqLockById(sip);
+					if(bsp != NULL)
+					{
+						b_store = create_byte_store_from_bsp (bsp);
+						mol = bsp->mol;
+						BioseqUnlock(bsp);
+					}
+				}
+			}
+			if(b_store != NULL)
+			{
+				if(mask_list->next == NULL)
+				{
+					c_store = b_store;
+					b_store = NULL;
+				}
+				else
+					c_store = BSDup(b_store);
+				MaskWithLowComplexity(c_store, slp, mol);
+				curr->data.ptrvalue = c_store;
+			}
+		}
+
+		mask_list = mask_list->next;
+	}
+
+	if(b_store != NULL)
+		BSFree(b_store);
+	return list;
+}
+
+/*******************************************************/
+
+static void PrintOutScore(SeqAlignPtr sap, Boolean is_aa, Int4Ptr PNTR matrix, ValNodePtr mask_loc)
+{
+	Int4 number, score;
+	Nlm_FloatHi bit_score, evalue; 
+        CharPtr eval_buff_ptr;
+	static Char eval_buff[10], bit_score_buff[10];
+	AlignSumPtr asp;
+	Int2 percent_identical, percent_positive;
+        ValNodePtr bs_list;
+        BioseqPtr q_bsp;
+        Int4 frame;
+        Uint1 code;
+        Uint1 repr;
+        ByteStorePtr seq_data;
+
+	printf("<pre>\n");
+	GetScoreAndEvalue(sap, &score, &bit_score, &evalue, &number);
+
+	eval_buff_ptr = eval_buff;
+	if (evalue < 1.0e-180) {
+		sprintf(eval_buff, "0.0");
+	} else if (evalue < 1.0e-99) {
+		sprintf(eval_buff, "%2.0le", evalue);
+		eval_buff_ptr++;	/* Knock off digit. */
+	} else if (evalue < 0.0009) {
+		sprintf(eval_buff, "%3.0le", evalue);
+	} else if (evalue < 0.1) {
+		sprintf(eval_buff, "%4.3lf", evalue);
+	} else if (evalue < 1.0) {
+		sprintf(eval_buff, "%3.2lf", evalue);
+	} else if (evalue < 10.0) {
+		sprintf(eval_buff, "%2.1lf", evalue);
+	} else {
+		sprintf(eval_buff, "%5.0lf", evalue);
+	}
+
+	if (bit_score > 9999) {
+		sprintf(bit_score_buff, "%4.3le", bit_score);
+	} else if (bit_score > 99.9) {
+		sprintf(bit_score_buff, "%4.0ld", (long) bit_score);
+	} else {
+		sprintf(bit_score_buff, "%4.1lf", bit_score);
+	}
+
+	if (number == 1) {
+		printf("Score = %s bits (%ld), Expect = %s<BR>", 
+			bit_score_buff, (long) score, eval_buff_ptr);
+	} else {
+		printf("Score = %s bits (%ld), Expect(%ld) = %s<BR>", 
+			bit_score_buff, (long) score, (long) number, eval_buff_ptr);
+	}
+	asp = MemNew(sizeof(AlignSum));
+	asp->matrix = NULL;
+        if (is_aa) {
+           if (matrix != NULL)
+              asp->matrix = matrix;
+           else
+              asp->matrix = load_default_matrix();
+	}
+	asp->is_aa = is_aa;
+	asp->totlen = 0;
+	asp->positive = 0;
+	asp->identical = 0;
+	asp->gaps = 0;
+        asp->master_sip = SeqIdDup(TxGetQueryIdFromSeqAlign(sap));
+        asp->target_sip = TxGetSubjectIdFromSeqAlign(sap);
+
+        if (mask_loc) { /* Mask the query sequence */
+           bs_list = CreateMaskByteStore (mask_loc);
+           q_bsp = BioseqLockById(asp->master_sip);
+           if (ISA_na(q_bsp->mol) && sap->segtype == SAS_STD) {
+              StdSegPtr ssp = (StdSegPtr) sap->segs;
+              frame = SeqLocStart(ssp->loc);
+              if (SeqLocStrand(ssp->loc) == Seq_strand_minus) {
+                 frame += SeqLocLen(ssp->loc);
+                 frame = -(1+(q_bsp->length - frame)%3);
+              } else {
+                 frame = (1+frame%3);
+              }
+           } else
+              frame = 0;
+           repr = q_bsp->repr;
+           seq_data = q_bsp->seq_data;
+           code = q_bsp->seq_data_type;
+           if (!replace_bytestore_data(q_bsp, bs_list, (Uint1)frame)) {
+              q_bsp->repr = repr;
+              q_bsp->seq_data = seq_data;
+              q_bsp->seq_data_type = code;
+           }
+           BioseqUnlock(q_bsp);
+        }
+
+        find_score_in_align(sap, 1, asp);
+
+	if (asp && asp->totlen > 0) {
+           Char sign1, sign2;           
+
+	   percent_identical = (100*asp->identical)/ (asp->totlen);
+	   percent_positive = (100*asp->positive)/ (asp->totlen);
+           if (asp->is_aa)
+              printf("Identities = %ld/%ld (%ld%%), Positives = %ld/%ld (%ld%%)", (long) asp->identical, (long) asp->totlen, percent_identical,
+                     (long) (asp->positive+asp->identical), (long)
+                     asp->totlen, (percent_identical+percent_positive));
+           else
+              printf("Identities = %ld/%ld (%ld%%)", (long) asp->identical, (long) asp->totlen, percent_identical);
+	   if (asp->gaps > 0) {
+		printf(", Gaps = %ld/%ld (%ld%%)<BR>", (long) asp->gaps, 
+			(long) asp->totlen, 
+				(long) (100*asp->gaps)/(asp->totlen));
+	   } else {
+	   		printf("<BR>");
+	   }
+           
+           sign1 = sign2 = '0';
+           if (asp->m_frame > 0) sign1 = '+';
+           else if (asp->m_frame < 0) sign1 = '-';
+           if (asp->t_frame > 0) sign2 = '+';
+           else if (asp->t_frame < 0) sign2 = '-';
+           if (sign1 != '0' && sign2 != '0')
+                 printf(" Frame = %c%d / %c%d", sign1, ABS(asp->m_frame),
+                        sign2, ABS(asp->t_frame));
+           else if (sign1 != '0')
+              printf(" Frame = %c%d", sign1, ABS(asp->m_frame));
+           else if (sign2 != '0')
+              printf(" Frame = %c%d", sign2, ABS(asp->t_frame));
+           else if (asp->m_strand != Seq_strand_unknown && asp->t_strand != Seq_strand_unknown) {
+              if (asp->m_strand != asp->t_strand)
+                 printf(" Strand = Plus / Minus");
+              else
+                 printf(" Strand = Plus / Plus");
+           }
+           printf("<BR><BR>");
+	}
+	printf("</pre>\n");		
+        SeqIdFree(asp->master_sip);
+        MemFree(asp);
+}
+
+static Int2 CreateRectAlign(SeqAlignPtr sap, PrymPtr PNTR rect, PrymPtr PNTR rectY, FloatHi scalex, FloatHi scaley, Int4 l1, Int4 l2, Int2 color, Int4 from, Int4 ffrom, Int4 to, Int4 tto)
+{
+	DenseDiagPtr ddp;
+	DenseSegPtr  dsp;
+	Int4         index1;
+	Int4         x1, x2, y1, y2;
+	Int2         k, sx, sy;
+	Boolean first = TRUE;
+
+	if (sap == NULL) {
+		return 0;
+	}
+	k = 0;
+
+	if (sap->segtype == SAS_DENDIAG) {
+		ddp = sap->segs;
+		x2 = y2 = 0;
+		first = TRUE;
+	    while (ddp != NULL) {
+			x1 = ddp->starts [0];
+			y1 = ddp->starts [1];
+			sx = ddp->strands[0];
+			sy = ddp->strands[1];
+			if (first) {
+				if (sx == Seq_strand_plus) {
+					x1 = ddp->starts[0] - from + 1;
+				} else {
+					x1 = to - (ddp->starts[0] +  ddp->len) + 1;
+				}
+				if (sy == Seq_strand_plus) {
+					y1 = ddp->starts[1] - from + 1;
+				} else {
+					y1 = tto - (ddp->starts[1] +  ddp->len) + 1;
+				}
+				rect[k] = MemNew(sizeof(Prym));
+				rect[k]->color = -1;
+				rect[k]->len = 0;
+				rectY[k] = MemNew(sizeof(Prym));
+				rectY[k]->color = -1;
+				rectY[k]->len = 0;
+			     if (x1 < y1) {
+				    rect[k]->len = (y1-x1)*scalex + 0.5;
+			     } else {
+				    rectY[k]->len = (x1-y1)*scalex + 0.5;
+			     }
+				 first = FALSE;
+				k++;
+			 }
+			rect[k] = MemNew(sizeof(Prym));
+			rect[k]->color = 0;
+			rect[k]->len = (x1 - x2)*scalex + 0.5;
+			rectY[k] = MemNew(sizeof(Prym));
+			rectY[k]->color = 0;
+			rectY[k]->len = (y1 - y2)*scaley + 0.5;
+			k++;
+		    x2 = ddp->starts [0] + ddp->len;
+		    y2 = ddp->starts [1] + ddp->len;
+			rect[k] = MemNew(sizeof(Prym));
+			rect[k]->color = color;
+			rect[k]->len = (x2 - x1)*scalex + 0.5;
+			rectY[k] = MemNew(sizeof(Prym));
+			rectY[k]->color = color;
+			rectY[k]->len = (y2 - y1)*scaley + 0.5;
+			k++;
+
+		      ddp = ddp->next;
+	    }
+		rect[k] = MemNew(sizeof(Prym));
+		rect[k]->color = 0;
+		if (sx != Seq_strand_minus) {
+			rect[k]->len = (to - x2)*scalex + 0.5;
+		} else {
+			rect[k]->len = (x1 - from +1)*scalex + 0.5;
+		}
+		rectY[k] = MemNew(sizeof(Prym));
+		rectY[k]->color = 0;
+		if (sy != Seq_strand_minus) {
+			rectY[k]->len = (tto - y2)*scaley + 0.5;
+		} else {
+			rectY[k]->len = (y1 - ffrom +1)*scaley + 0.5;
+		}
+		k++;
+	} else if (sap->segtype == SAS_DENSEG) {
+		dsp = sap->segs;
+		k = 0;
+		for (index1=0; index1 < dsp->numseg; index1++) {
+			x1 = dsp->starts[2*index1];
+			y1 = dsp->starts[2*index1+1];
+			sx = dsp->strands[2*index1];
+			sy = dsp->strands[2*index1+1];
+			x2 = x1 + dsp->lens[index1];
+			y2 = y1 + dsp->lens[index1];
+			if (index1 == 0) {
+				if (sx == Seq_strand_minus) {
+					x1 = to - (dsp->starts[0] +  dsp->lens[0]) + 1;
+				} else {
+					x1 = dsp->starts[0] - from + 1;
+				}
+				if (sy == Seq_strand_minus) {
+					y1 = tto - (dsp->starts[1] + dsp->lens[0]) + 1;
+				} else {
+					y1 = dsp->starts[1] - ffrom + 1;
+				}
+				rect[k] = MemNew(sizeof(Prym));
+				rect[k]->color = -1;
+				rect[k]->len = 0;
+				rectY[k] = MemNew(sizeof(Prym));
+				rectY[k]->color = -1;
+				rectY[k]->len = 0;
+				if (x1 < y1) {
+					rect[k]->len = (y1-x1)*scalex + 0.5;
+				} else {
+				    rectY[k]->len = (x1-y1)*scalex + 0.5;
+				}
+				k++;
+				rect[k] = MemNew(sizeof(Prym));
+				rect[k]->color = 0;
+				rect[k]->len = x1*scalex + 0.5;
+				rectY[k] = MemNew(sizeof(Prym));
+				rectY[k]->color = 0;
+				rectY[k]->len = y1*scalex + 0.5;
+				k++;
+			}
+			rect[k] = MemNew(sizeof(Prym));
+			if (x1 == -1) {
+				rect[k]->color = 3;
+			} else {
+				rect[k]->color = color;
+			}
+			rect[k]->len = dsp->lens[index1]*scalex + 0.5;
+			rectY[k] = MemNew(sizeof(Prym));
+			if (y1 == -1) {
+				rectY[k]->color = 3;
+			} else {
+				rectY[k]->color = color;
+			}
+			rectY[k]->len = dsp->lens[index1]*scalex + 0.5;
+			k++;
+		}
+		rect[k] = MemNew(sizeof(Prym));
+		rect[k]->color = 0;
+		if (sx == Seq_strand_minus) {
+			rect[k]->len = (x1 - from +1)*scalex + 0.5;
+		} else {
+			rect[k]->len = (to - x2)*scalex + 0.5;
+		}
+		rectY[k] = MemNew(sizeof(Prym));
+		rectY[k]->color = 0;
+		if (sy == Seq_strand_minus) {
+			rectY[k]->len = (y1 - ffrom +1)*scaley + 0.5;
+		} else {
+			rectY[k]->len = (tto - y2)*scaley + 0.5;
+		}
+		k++;
+	} else if (sap->segtype == SAS_STD) {
+           StdSegPtr ssp = sap->segs;
+           SeqLocPtr slp;
+
+           while (ssp) {
+              slp = ssp->loc;
+              if (!slp || !slp->next) {
+                 ssp = ssp->next;
+                 continue;
+              }
+              if (slp->choice == SEQLOC_EMPTY) {
+                 x1 = x2 = -1;
+                 sx = Seq_strand_unknown;
+              } else {
+                 x1 = SeqLocStart(slp);
+                 sx = SeqLocStrand(slp);
+                 x2 = SeqLocStop(slp) + 1;
+              }
+              if (slp->next->choice == SEQLOC_EMPTY) {
+                 y1 = y2 = -1;
+                 sy = Seq_strand_unknown;
+              } else {
+                 y1 = SeqLocStart(slp->next);
+                 sy = SeqLocStrand(slp->next);
+                 y2 = SeqLocStop(slp->next) + 1;
+              }
+
+              if (first) { 
+                 if (sx == Seq_strand_plus) {
+                    x1 -= from - 1;
+                 } else if (sx == Seq_strand_minus) {
+                    x1 = to - x2 + 1;
+                 }
+                 if (sy == Seq_strand_plus) {
+                    y1 -= ffrom - 1;
+                 } else if (sy == Seq_strand_minus){
+                    y1 = tto - y2 + 1;
+                 }
+
+                 rect[k] = MemNew(sizeof(Prym));
+                 rect[k]->color = -1;
+                 rect[k]->len = 0;
+                 rectY[k] = MemNew(sizeof(Prym));
+                 rectY[k]->color = -1;
+                 rectY[k]->len = 0;
+                 if (y1*scaley>x1*scalex)
+                    rect[k]->len = y1*scaley - x1*scalex + 0.5;
+                 else
+                    rectY[k]->len = x1*scalex - y1*scaley + 0.5;
+                 first = FALSE;
+                 k++;
+                 rect[k] = MemNew(sizeof(Prym));
+                 rect[k]->color = 0;
+                 rect[k]->len = x1*scalex + 0.5;
+                 rectY[k] = MemNew(sizeof(Prym));
+                 rectY[k]->color = 0;
+                 rectY[k]->len = y1*scaley + 0.5;
+                 k++;
+              }
+              rect[k] = MemNew(sizeof(Prym));
+              if (x1 == -1) {
+                 rect[k]->color = 3;
+                 rect[k]->len = SeqLocLen(slp->next)*scaley + 0.5;
+              } else {
+                 rect[k]->color = color;
+                 rect[k]->len = SeqLocLen(slp)*scalex + 0.5;
+              }
+
+              rectY[k] = MemNew(sizeof(Prym));
+              if (y1 == -1) {
+                 rectY[k]->color = 3;
+                 rectY[k]->len = SeqLocLen(slp)*scalex + 0.5;
+              } else {
+                 rectY[k]->color = color;
+                 rectY[k]->len = SeqLocLen(slp->next)*scaley + 0.5;
+              }
+              k++;
+              ssp = ssp->next;
+           }
+           rect[k] = MemNew(sizeof(Prym));
+           rect[k]->color = 0;
+           if (sx != Seq_strand_minus) {
+              rect[k]->len = (to - x2)*scalex + 0.5;
+           } else {
+              rect[k]->len = (x1 - from +1)*scalex + 0.5;
+           }
+           rectY[k] = MemNew(sizeof(Prym));
+           rectY[k]->color = 0;
+           if (sy != Seq_strand_minus) {
+              rectY[k]->len = (tto - y2)*scaley + 0.5;
+           } else {
+              rectY[k]->len = (y1 - ffrom +1)*scaley + 0.5;
+           }
+           k++;
+        }
+
+	return k;
+}
+
+static void DrawRectAlign(PrymPtr PNTR rect, Int2 k, Int2 color, Int2 height, Int2 index)
+{
+	Int2 l;
+	
+	for (l=0; l < k; l++) {
+		if (rect[l]->len <= 0) {
+			if (l == 0 && rect[1] && rect[1]->len == 0) {
+				printf("<img\n height=%d width=1 src='images/00.gif'>", height);
+			}
+                        MemFree(rect[l]);
+			continue;
+		}
+		if (rect[l]->len-1 == 0) {
+			rect[l]->len++;
+		}
+		if (rect[l]->color == -1) {
+			printf("<img\n height=2 src='images/0.gif'");
+			printf(" width=%d>", rect[l]->len);
+		} else if (rect[l]->color == 3) {
+			if (rect[l+1]->color == rect[l]->color) {
+				printf("<img\n height=5 src='images/3.gif'");
+				printf(" width=%d>", rect[l]->len);
+			} else {
+				printf("<img\n height=5 src='images/3.gif'");
+				printf(" width=%d>", rect[l]->len-1);
+				printf("<img\n height=%d width=1 src='images/00.gif'>", height);
+			}
+		} else if (rect[l]->color == 0) {
+			if (rect[l+1] &&  rect[l+1]->color != -1) {
+				printf("<img\n height=2 src='images/00.gif'");
+				printf(" width=%d>", rect[l]->len-1);
+				printf("<img\n height=%d width=1 src='images/00.gif'>", height);
+			} else {
+				printf("<img\n height=2 src='images/00.gif'");
+				printf(" width=%d>", rect[l]->len);
+			}
+		} else if (rect[l]->len > 0) {
+			if (rect[l+1]->color == rect[l]->color) {
+				if (index != -1) {
+				printf("<A HREF=#%d><img height=%d src='images/%d.gif' BORDER=0", 
+													index, height, color);
+					printf(" width=%d></a>", rect[l]->len);
+				} else {
+					printf("<img height=%d src='images/%d.gif'", 
+													height, color);
+					printf(" width=%d>", rect[l]->len);
+				}
+			} else {
+				if (index != -1) {
+				printf("<A HREF=#%d><img height=%d src='images/%d.gif' BORDER=0",
+						index, height, color);
+					printf(" width=%d></a>", rect[l]->len-1);
+				} else {
+					printf("<img height=%d src='images/%d.gif'",
+						height, color);
+					printf(" width=%d>", rect[l]->len-1);
+				}
+				printf("<img\n height=%d width=1 src='images/00.gif'>", height);
+			}
+		}
+                MemFree(rect[l]);
+	}
+}
+
+static void PrintRectAlign(PrymPtr PNTR rect, Int2 k, Int2 color, Int2 height, Int2 index)
+{
+	Int2 l;
+	
+	for (l=0; l < k; l++) {
+		if (rect[l]->len <= 0) {
+			continue;
+		}
+		if (rect[l]->len-1 == 0) {
+			rect[l]->len++;
+		}
+		if (rect[l]->color == -1) {
+			printf("images/0.gif");
+			printf(" width=%d>", rect[l]->len);
+		} else if (rect[l]->color == 3) {
+			if (rect[l+1]->color == rect[l]->color) {
+				printf("images/3.gif");
+				printf(" width=%d", rect[l]->len);
+			} else {
+				printf("images/3.gif");
+				printf(" width=%d>", rect[l]->len-1);
+			}
+		} else if (rect[l]->color == 0) {
+			if (rect[l+1] &&  rect[l+1]->color != -1) {
+				printf(" width=%d>", rect[l]->len-1);
+			} else {
+				printf(" width=%d>", rect[l]->len);
+			}
+		} else if (rect[l]->len > 0) {
+			if (rect[l+1]->color == rect[l]->color) {
+				if (index != -1) {
+					printf(" RECT:width=%d></a>", rect[l]->len);
+				} else {
+					printf(" RECT:width=%d>", rect[l]->len);
+				}
+			} else {
+				if (index != -1) {
+					printf(" RECT width=%d></a>", rect[l]->len-1);
+				} else {
+					printf("RECT width=%d>", rect[l]->len-1);
+				}
+			}
+		}
+	}
+}
+
+#define LOCAL_BUFLEN 255
+static BioseqPtr FindSeqByAccession(CharPtr accver, Int2 id_num, Boolean is_na)
+{
+   BioseqPtr bsp = NULL;
+
+#ifdef NCBI_ENTREZ_CLIENT
+   CharPtr accession;
+   Int4 version=0, gi, number;
+   SeqIdPtr sip = NULL;
+   TextSeqIdPtr tsip;
+   PDBSeqIdPtr  psip;
+   SeqPortPtr spp;
+   Int2 retval, buf_length=512;
+   Uint1 buf[512];
+
+   ID1BioseqFetchEnable ("wblast2", TRUE);
+      
+   if ((gi = atoi(accver)) == 0) {
+      accession = StringTokMT(accver, ".", &accver);
+      
+      if (accver)
+         version = atoi(accver);
+
+      if((sip = ValNodeNew (NULL)) == NULL)
+         return NULL;
+      if((tsip = TextSeqIdNew ()) == NULL)
+         return NULL;
+      
+      tsip->accession = StringSave(accession);
+      tsip->version = version;
+      /* GenBank, EMBL, and DDBJ. */
+      sip->choice = SEQID_GENBANK;
+      sip->data.ptrvalue = (Pointer) tsip;
+
+      gi = ID1FindSeqId (sip);
+      
+      if (gi == 0) {
+         /* SwissProt. */
+         sip->choice = SEQID_SWISSPROT;
+         gi = ID1FindSeqId (sip);
+      }
+      if (gi == 0) {
+         /* PIR */
+         sip->choice = SEQID_PIR;
+         gi = ID1FindSeqId (sip);
+      }
+      
+      if (gi == 0) {
+         /* PRF */
+         sip->choice = SEQID_PRF;
+         gi = ID1FindSeqId (sip);
+      }
+      
+      if (gi == 0) {
+         /* OTHER, probably 'ref' */
+         sip->choice = SEQID_OTHER;
+        gi = ID1FindSeqId (sip);
+      }
+      
+      if(gi == 0) {
+         /* OK. We failed to find gi using string as TextSeqId. Now trying
+            last time - with PDBSeqIdPtr */
+         
+         if((psip = PDBSeqIdNew()) == NULL)
+            return NULL;
+         
+         sip->choice = SEQID_PDB;
+         tsip = TextSeqIdFree(tsip);
+         sip->data.ptrvalue = psip;
+         
+         psip->mol = accession;
+         psip->chain = version;
+         
+         gi = ID1FindSeqId (sip);
+      }
+    
+      sip = SeqIdFree(sip);
+   }
+   if (gi > 0) {
+      ValNodeAddInt(&sip, SEQID_GI, gi);
+      bsp = BioseqLockById(sip);
+   } 
+
+   if (bsp == NULL)
+      return NULL;
+   
+   if (ISA_na(bsp->mol) != is_na) {
+      BioseqUnlock(bsp);
+      return NULL;
+   }
+
+   /* We need to keep this bioseq to preserve the protein information for the 
+      CDS translation feature. However we also need to pack the sequence data,
+      so bsp->seq_data has to be modified.
+   */
+   if (ISA_na(bsp->mol)) {
+      spp = SeqPortNew(bsp, 0, -1, Seq_strand_plus, 
+                       Seq_code_iupacna);
+      bsp->seq_data_type = Seq_code_iupacna;
+   } else {
+      spp = SeqPortNew(bsp, 0, -1, Seq_strand_unknown, 
+                       Seq_code_ncbieaa);
+      bsp->seq_data_type = Seq_code_ncbieaa;
+   }
+    
+   SeqPortSet_do_virtual(spp, TRUE);
+   number = 0;
+   
+   bsp->repr = Seq_repr_raw;
+   bsp->seq_data = BSNew(bsp->length);
+
+   while (number < bsp->length) {
+      retval = SeqPortRead(spp, buf, buf_length);
+      if (retval < 0)
+         continue;
+      if (retval == 0)
+         break;
+      BSWrite(bsp->seq_data, buf, retval);
+      number += retval;
+   }
+    
+   SeqPortFree(spp);
+   BioseqPack(bsp);
+   ID1BioseqFetchDisable();
+   
+#endif
+
+    return bsp;
+}
+
+static void BLASTOptionValidateHTML(BLAST_OptionsBlkPtr options, CharPtr progname, CharPtr seq1, CharPtr seq2, CharPtr one, CharPtr two, Boolean is_prot, Int2 mtrx, Int2 from, Int2 to, Int2 ffrom, Int2 tto, Int2 filter, Int2 pagecount)
+{
+    Int2 status;
+    ValNodePtr error_return=NULL;
+    
+    status = BLASTOptionValidateEx(options, progname, &error_return);
+    if (status != 0) {
+        Blast2SeqMainPage(NULL, seq1, seq2, one, two, error_return, is_prot, options, mtrx, from, to, ffrom, tto, filter, pagecount);
+    }
+    return;
+}
+
+static void PrintParam(Boolean is_prot, Int2 mtrx, Int2 ma, Int2 ms, BLAST_OptionsBlkPtr options, CharPtr seq_2, CharPtr seq_1, CharPtr one, CharPtr two, BioseqPtr query_bsp, BioseqPtr subject_bsp, Int4 len1, Int4 len2, Int4 from, Int4 to, Int4 ffrom, Int4 tto, Int2 pagecount)
+{
+    ValNodePtr vnp;
+    CharPtr s;
+    static Char buf[41];
+    Int4 gi;
+
+    printf("<FORM NAME= bl2 method=\"POST\" action="    
+#if defined (BL2SEQ_STANDALONE) && defined (NCBI_ENTREZ_CLIENT)
+           "\"wblast2_cs.cgi"
+#else 
+           "\"wblast2.cgi"
+#endif
+           "?%d\" enctype=\"multipart/form-data\">\n\n", pagecount);
+
+    printf("<INPUT TYPE=hidden name=\"page\" value=\"%d\">\n", pagecount+1);
+    if (is_prot == TRUE) {
+#if defined (BL2SEQ_STANDALONE)
+        printf("<A HREF=docs/options.html#matrix>Matrix</A>\n");
+#else
+        printf("<A HREF=http://www.ncbi.nlm.nih.gov/BLAST/options.html#matrix TARGET=one>Matrix</A>\n");
+#endif
+        printf("<select name=\"matrix\" onChange=\"update_mtrx(this)\">\n");
+        
+        printf("<option value=0>BLOSUM62\n");
+        printf("<option value=1%s>PAM30\n", (mtrx == 1) ? " SELECTED" : "");
+        printf("<option value=2%s>PAM70\n", (mtrx == 2) ? " SELECTED" : "");
+        printf("<option value=3%s>PAM250\n", (mtrx == 3) ? " SELECTED" : "");
+        printf("<option value=4%s>BLOSUM90\n", (mtrx == 4) ? " SELECTED" : "");
+        printf("<option value=5%s>BLOSUM50\n", (mtrx == 5) ? " SELECTED" : "");
+        printf("</select>\n");
+    } else {
+       printf("Match:<INPUT TYPE=text name=match size=2 value=%d>\n", ma); 
+       printf("Mismatch:<INPUT TYPE=text name=msmatch size=2 value=%d>\n", ms);
+    }
+    printf("gap open:<INPUT TYPE=text name=gopen size=2 value=%d>\n", options->gap_open);
+    printf("gap extension: <INPUT TYPE=text size=2 name=\"gext\" value=%d> <BR>\n", options->gap_extend);
+    printf("x_dropoff: <INPUT TYPE=text size=2 name=\"dropoff\" value=\"%d\">\n", options->gap_x_dropoff);
+    printf("expect:<INPUT TYPE=text size=4 name=\"expect\" value=\"%f\">\n", options->expect_value);
+    printf("wordsize: <INPUT type=text size=2 name=\"word\" "); 
+    printf("value=%d>\n\n", options->wordsize);
+#if defined (BL2SEQ_STANDALONE)
+    printf("<a href=docs/newoptions.html#filter>Filter</a>");
+#else
+    printf("<a href=http://www.ncbi.nlm.nih.gov/blast/newoptions.html#filter>Filter</a>");
+#endif
+
+    printf(" <INPUT TYPE=checkbox NAME=Filter VALUE=1");
+    if (options->filter == 1) {
+        printf(" CHECKED>\n");
+    } else {
+        printf(">\n");
+    }
+    printf("<INPUT TYPE=hidden name=\"program\" value=\"%s\">\n",
+           options->program_name);
+    
+    printf("<INPUT TYPE=hidden name=\"matrix\" value=\"%d\">\n", mtrx);
+    
+    printf("<INPUT TYPE=submit VALUE=Align><HR>\n");
+    if (seq_1 != NULL && *seq_1 != NULLB) {
+        printf("<INPUT TYPE=hidden name=\"seq\" value=\"");
+        for (s = seq_1; *s != '\0'; s++) {
+            if (*s == '>') {
+                printf("&gt;");
+            } else {
+                printf("%c", *s);
+            }
+        }
+        printf("\">\n");
+    } else if (one != NULL) {
+        printf("<INPUT TYPE=hidden name=\"one\" value=\"%s\">\n", one);
+    }
+    if (seq_2 != NULL && *seq_2 != NULLB) {
+        printf("<INPUT TYPE=hidden name=\"sseq\" value=\"");
+        for (s = seq_2; *s != '\0'; s++) {
+            if (*s == '>') {
+                printf("&gt;");
+            } else {
+                printf("%c", *s);
+            }
+        }
+        printf("\">\n");
+    } else if (two != NULL) {
+        printf("<INPUT TYPE=hidden name=\"two\" value=\"%s\">\n", two);
+    }
+    printf("<INPUT TYPE=hidden name=\"from\" value=\"%d\">\n", from);
+    printf("<INPUT TYPE=hidden name=\"to\" value=\"%d\">\n", to);
+    printf("<INPUT TYPE=hidden name=\"ffrom\" value=\"%d\">\n", ffrom);
+    printf("<INPUT TYPE=hidden name=\"tto\" value=\"%d\">\n", tto);
+    printf("<TABLE>\n");
+    printf("<TR><TD><strong> Sequence 1</strong></TD>\n");
+    if ((gi = GetGIForSeqId(SeqIdFindBest(query_bsp->id, SEQID_GI))) != 0) {
+        printf("<TD>gi<A HREF=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=%ld> %ld</A></TD>", gi, gi);
+    } else {
+        SeqIdWrite(query_bsp->id, buf, PRINTID_FASTA_LONG, 40);
+        printf("<TD>%s</TD>", buf);
+    }
+    for (vnp=query_bsp->descr; vnp; vnp=vnp->next) {
+        if (vnp->choice == Seq_descr_title) {
+            printf("<TD>%s</TD>", vnp->data.ptrvalue);
+            break;
+        }
+    }
+    if (vnp == NULL) {
+        printf("<TD></TD>");
+    }
+    printf("<TD><strong>Length</strong></TD><TD>%ld</TD>\n", len1);
+    if (from != 0 || to != 0) {
+        printf("<TD>(%ld .. %ld)</TD>\n", from, to);
+    }
+    printf("</TR><TR>\n");
+    printf("<TR><TD><strong> Sequence 2</strong></TD>\n");
+    if ((gi = GetGIForSeqId(SeqIdFindBest(subject_bsp->id, SEQID_GI))) != 0) {
+        printf("<TD>gi <A HREF=http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=%ld>%ld</A></TD>", gi, gi);
+    } else {
+        SeqIdWrite(subject_bsp->id, buf, PRINTID_FASTA_LONG, 40);
+        printf("<TD>%s</TD>", buf);
+    }
+    for (vnp=subject_bsp->descr; vnp; vnp=vnp->next) {
+        if (vnp->choice == Seq_descr_title) {
+            printf("<TD>%s</TD>", vnp->data.ptrvalue);
+            break;
+        }
+    }
+    if (vnp == NULL) {
+        printf("<TD></TD>");
+    }
+    printf("<TD><strong>Length</strong></TD><TD>%ld</TD>\n", len2);
+    if (ffrom != 0 || tto != 0) {
+        printf("<TD>(%ld .. %ld)</TD>\n", ffrom, tto);
+    }
+    printf("</TR></TABLE>\n");
+
+    return;
+}
+
+#ifndef BL2SEQ_STANDALONE
+/** Thread to take care of log messages when termination by signal */
+static void* ConnectionThreadRun(void *p)
+{
+   int nfds;
+   int rc;
+   struct pollfd *fds=NULL;
+
+   nfds = 1;
+
+   fds = (struct pollfd *) 
+      malloc( nfds*sizeof(struct pollfd) );
+
+
+   fds[0].fd = fileno(stdout);
+   fds[0].events = POLLOUT;
+   fds[0].revents = 0;
+
+   poll(NULL, 0, 2000);
+
+   while (run_status != WBLAST2_DONE) {
+      if (sigflag) {
+         int signo = GetSignal();
+
+         if (signo == SIGXCPU) {
+            if (run_status == WBLAST2_FORMAT) {
+               /* Ignore CPU limit if formatting has already started */
+               signo = 0;
+            } else {
+               printf("<HTML>\n<HEAD>\n<TITLE>\nTime Expired\n</TITLE>\n</HEAD>\n");
+               printf("<BODY>\n<H1>\nTime expired\n</H1>\n<HR>\n</BODY>\n</HTML>\n");
+               fflush(NULL);
+            }
+         }
+         if (signo) {
+            logmsg(signo);
+            poll(NULL, 0, 1000);
+            exit(signo);
+         }
+      }
+
+      /* If no signal has been received yet, test the stdout socket */
+      rc = poll(fds, nfds, 1000);
+
+      if (run_status == WBLAST2_DONE)
+         break;
+
+      if (rc < 0 || 
+          (fds[0].revents & (POLLHUP | POLLNVAL | POLLERR))) {
+         logmsg(fds[0].revents);
+         close(fds[0].fd);
+         abort();
+      } else if (run_status == WBLAST2_SEARCH) {
+          char buffer[4096];
+          memset(buffer, ' ', 4095);
+          buffer[4095] = NULLB;
+          /*strcpy(buffer, "      ");*/
+          
+          fprintf(stdout, "<!--%s-->\n", buffer);
+          fflush(stdout);
+      }
+      if (run_status != WBLAST2_DONE) /* Sleep 4 seconds */
+         poll(NULL, 0, 4000);
+   }
+   
+   return NULL;
+}
+#endif
+
+#define BL2SEQ_CPU_LIMIT 240
+
+Int2 Main(void)
+{
+    SeqEntryPtr sep;
+    BioseqPtr fake_bsp, query_bsp = NULL, subject_bsp = NULL;
+    SeqIntPtr sip1, sip2;
+    Int2 index = 0;
+    Int4 gopen, gext, dropoff, ma=0, ms=0;
+    Int4 from=0, to=0, ffrom=0, tto=0;
+    Int2 wordsize, filter=0;
+    Int2 mtrx = 0, color=1;
+    SeqAlignPtr seqalign, sap, sapnext;
+    SeqAnnotPtr hsat= NULL, sat, satnext;
+    FloatHi	expect;
+    Boolean is_prot=FALSE, is_aa1=FALSE, is_aa2=FALSE, is_na1=TRUE, is_na2=TRUE;
+    CharPtr seq_1=NULL, seq_2=NULL, c1, c2, chptr;
+    CharPtr sq_1=NULL, sq_2=NULL, one=NULL, two=NULL, sbuf, progname;
+    static Char mbuf[12];
+    BLAST_OptionsBlkPtr options = NULL;
+    Int4 ll, len1, len2, txoption;
+    SeqIdPtr sip;
+    Int4Ptr PNTR txmatrix;
+    BLAST_MatrixPtr blast_matrix;
+    SeqPortPtr spp;
+    Uint1 code1, code2;
+    ValNodePtr vnp, error_return=NULL;
+    FloatHi       scalex, scaley;
+    DenseDiagPtr ddp;
+    DenseSegPtr  dsp;
+    StdSegPtr    ssp;
+    Int4         index1, i2;
+    Int4         x, y, xx, yy;
+    Int2         k, x_factor, y_factor;
+    static PrymPtr PNTR rect;
+    static PrymPtr PNTR rectY;
+    SeqLocPtr    slp1=NULL, slp2=NULL, slp, sl, qslp = NULL;
+    Uint1        align_type;
+    
+    ValNodePtr	   other_returns, mask, mask_head;
+    CharPtr		   buffer;
+    BLAST_KarlinBlkPtr ka_params=NULL, ka_gap_params=NULL;
+    TxDfDbInfoPtr      dbinfo = NULL;
+    BlastTimeKeeper    time_keeper;
+    
+    WWWBlastInfoPtr theInfo;
+    ReadDBFILEPtr rdfp;
+    Int4 dbseq_num;
+    CharPtr dbname;
+    CharPtr error_msg;
+    Int2 pagecount = 0;
+    Boolean is_megablast = FALSE;
+    CharPtr rid = NULL, database = NULL;
+    sigset_t sigset;
+    struct sigaction sa;
+#ifndef BL2SEQ_STANDALONE
+    TNlmThread connection_thread = NULL;
+    void *thrstat;
+    CharPtr program_log, user_IP;
+    int pid, time_start, results_size = 0;
+#endif
+
+#ifdef RLIMIT_CPU
+    struct rlimit rl;
+    
+#ifdef SIGXCPU
+    sa.sa_flags = SA_RESTART;
+    sa.sa_handler = sighandler;
+    sigaction(SIGXCPU, &sa, NULL);
+#endif
+    getrlimit(RLIMIT_CPU, &rl);
+    rl.rlim_cur = BL2SEQ_CPU_LIMIT;
+    rl.rlim_max = BL2SEQ_CPU_LIMIT + 120;
+    setrlimit(RLIMIT_CPU, &rl);
+#endif
+
+    /* mask all signals when in signal handler */
+    sigfillset(&sigset);
+    sa.sa_mask = sigset;
+
+    /* Handle SIGPIPE */
+    sa.sa_flags = SA_RESTART;
+    sa.sa_handler = sighandler;
+    sigaction(SIGPIPE, &sa, NULL);
+
+    if (!SeqEntryLoad())
+        return 1;
+    
+    UseLocalAsnloadDataAndErrMsg ();
+    
+    ErrSetMessageLevel(SEV_WARNING);
+    
+    PrepareSigmask();
+
+    /* This function will read posting data, set-up config file and
+       write small message into logfile (if it exists) */
+    
+    theInfo = MemNew(sizeof(WWWBlastInfo));
+    
+    if(WWWGetArgs(&theInfo->info) != WWWErrOk) {
+        WWWInfoFree(theInfo->info);
+        MemFree(theInfo);
+        Blast2SeqMainPage(NULL, NULL, NULL, NULL, NULL, NULL, FALSE, 
+                          NULL, 0, 0, 0, 0, 0, 1, 0);
+        return 1;    
+    }
+    if((chptr = WWWGetQuery(theInfo->info)) == NULL || *chptr == NULLB) {
+        WWWInfoFree(theInfo->info);
+        MemFree(theInfo);
+        Blast2SeqMainPage(NULL, NULL, NULL, NULL, NULL, NULL, FALSE, 
+                          NULL, 0, 0, 0, 0, 0, 1, 0);
+    }
+    
+    if(getenv("DEBUG_COMMAND_LINE") != NULL) {
+        FILE *fd;
+        fd = FileOpen("__web.in", "w");
+        fprintf(fd, "%s", ((WWWInfoDataPtr)theInfo->info)->query);
+        FileClose(fd);
+    }
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "PROGRAM")) != NULL)
+        theInfo->program = StringSave(chptr);
+    else if ((chptr = WWWGetValueByName(theInfo->info, "PROT")) != NULL)
+        theInfo->program = StringSave(chptr);
+    else
+        theInfo->program = StringSave("blastn");
+    
+    theInfo->align_type = 
+        BlastGetTypes(theInfo->program, &theInfo->query_is_na, 
+                      &theInfo->db_is_na);
+    
+    is_aa1 = !theInfo->query_is_na;
+    is_aa2 = !theInfo->db_is_na;
+    is_prot = (is_aa1 || is_aa2);
+    
+    progname = theInfo->program;
+    
+    if ((chptr = WWWGetValueByName(theInfo->info, "MEGABLAST")) != NULL)
+       is_megablast = TRUE;
+    options = BLASTOptionNewEx(progname, TRUE, is_megablast);
+    
+    if ((chptr = WWWGetValueByName(theInfo->info, "PAGE")) != NULL)
+        pagecount = atoi(chptr);
+    
+    if ((chptr = WWWGetValueByName(theInfo->info, "GOPEN")) != NULL &&
+        StringStr(chptr, "default") == NULL)
+        gopen = atoi(chptr);
+    else
+        gopen = -1;
+    
+    if ((chptr = WWWGetValueByName(theInfo->info, "GEXT")) != NULL &&
+        StringStr(chptr, "default") == NULL)
+        gext = atoi(chptr);
+    else
+        gext = -1;
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "DROPOFF")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        dropoff = atoi(chptr);
+    else
+        dropoff = 50;
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "EXPECT")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        expect = atof(chptr);
+    else
+        expect = 10;
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "MATCH")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        ma = atoi(chptr);
+    else if (!StrCmp(progname, "blastn"))
+        ma = 1;
+    if((chptr = WWWGetValueByName(theInfo->info, "MSMATCH")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        ms = atoi(chptr);
+    else if (!StrCmp(progname, "blastn"))
+        ms = -2;
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "FROM")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        from = atoi(chptr);
+    else
+        from = 0;
+    if((chptr = WWWGetValueByName(theInfo->info, "FFROM")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        ffrom = atoi(chptr);
+    else
+        ffrom = 0;
+    if((chptr = WWWGetValueByName(theInfo->info, "TO")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        to = atoi(chptr);
+    else
+        to = 0;
+    if((chptr = WWWGetValueByName(theInfo->info, "TTO")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        tto = atoi(chptr);
+    else
+        tto = 0;
+
+    if((chptr = WWWGetValueByName(theInfo->info, "STRAND")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        options->strand_option = atoi(chptr);
+    else
+        options->strand_option = Seq_strand_both;
+
+#ifdef NCBI_ENTREZ_CLIENT
+    one = WWWGetValueByName(theInfo->info, "ONE");
+    two = WWWGetValueByName(theInfo->info, "TWO");
+#endif
+    options->cpu_limit = BL2SEQ_CPU_LIMIT;
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "WORD")) != NULL &&
+       StringStr(chptr, "default") == NULL)
+        wordsize = atoi(chptr);
+    else if (!is_megablast)
+        wordsize = (is_prot == TRUE) ? 3 : 11;
+    else {
+        wordsize = 28;
+    }
+
+    if (WWWGetValueByName(theInfo->info, "FILTER") != NULL)
+        filter =1;
+    
+    run_status = WBLAST2_SEARCH;
+
+#ifndef BL2SEQ_STANDALONE
+    /** fire thread testing connection; not done in the standalone 
+        WWW server package */
+    connection_thread = NlmThreadCreateEx(ConnectionThreadRun, NULL, 
+                           THREAD_RUN|THREAD_BOUND, eTP_Default, NULL, NULL);
+#endif
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "SEQ")) == NULL ||
+       *chptr == NULLB)
+        chptr = WWWGetValueByName(theInfo->info, "SEQFILE1");
+    
+    if (chptr) {
+       while (IS_WHITESP(*chptr))
+          chptr++;
+    }
+    if (chptr && *chptr != NULLB)
+       c1 = StringSave(chptr);
+    else
+       c1 = NULL;
+
+    if (c1 && *c1 != '>') {
+        sbuf = MemNew(StringLen(c1)+8);
+        sprintf(sbuf, ">seq_1\n%s", c1);
+        seq_1 = StringSave(sbuf);
+        MemFree(c1);
+        c1 = seq_1;
+        MemFree(sbuf);
+    }
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "SSEQ")) == NULL || 
+       *chptr == NULLB)
+        chptr = WWWGetValueByName(theInfo->info, "SEQFILE2");
+    
+    if (chptr) {
+       while (IS_WHITESP(*chptr))
+          chptr++;
+    }
+    if (chptr && *chptr != NULLB)
+        c2 = StringSave(chptr);
+    else 
+        c2 = NULL;
+    
+    if (c2 && *c2 != '>') {
+        sbuf = MemNew(StringLen(c2)+8);
+        sprintf(sbuf, ">seq_2\n%s", c2);
+        seq_2 = StringSave(sbuf);
+        MemFree(c2);
+        c2 = seq_2;
+        MemFree(sbuf);
+    }
+    seq_1 = c1;
+    seq_2 = c2;
+    if (c1 && c2 && StrNCmp(c1, c2, 6) == 0) {
+        if (*c1 == '>')
+            seq_1 = seq_1 + 1;
+        sbuf = Malloc(StringLen(seq_1)+4);
+        sprintf(sbuf, ">1_%s", seq_1);
+        seq_1 = StringSave(sbuf);
+        sbuf = MemFree(sbuf);
+        MemFree(c1);
+        if (*c2 == '>')
+            seq_2 = seq_2 + 1;
+        sbuf = Malloc(StringLen(seq_2)+4);
+        sprintf(sbuf, ">2_%s",seq_2);
+        seq_2 = StringSave(sbuf);
+        MemFree(sbuf);
+        MemFree(c2);
+    }
+    
+    if (seq_1 != NULL) {
+        sep = FastaToSeqBuff(seq_1, &sq_1, !is_aa1);
+        query_bsp = (BioseqPtr) sep->data.ptrvalue;
+        is_na1 = FastaCheckDna(seq_1);
+    } else if (one != NULL && *one != NULLB) {
+       if ((rid = WWWGetValueByName(theInfo->info, "RID")) != NULL) {
+#ifndef BL2SEQ_STANDALONE
+          /* Get the query sequence from the QBlast results */
+          sip = SeqIdParse(one);
+          
+          QBlastGetResultsEx(rid, NULL, &query_bsp, NULL, &database, NULL,
+                             NULL, sip);
+#endif
+          if (!query_bsp) {
+             error_msg = "The query sequence is not found";
+             Blast2SeqMainPage(error_msg, seq_1, seq_2, 
+                               one, two, NULL, is_prot, options, mtrx,
+                               from, to, ffrom, tto, filter, pagecount);
+          }
+       } else {
+          if ((query_bsp = FindSeqByAccession(one, 1, !is_aa1)) == NULL) {
+             error_msg = "The first sequence accession is not found";
+             Blast2SeqMainPage(error_msg, seq_1, seq_2, 
+                               one, two, NULL, is_prot, options, mtrx,
+                               from, to, ffrom, tto, filter, pagecount);
+          }
+       }
+       if (query_bsp)
+          is_na1 = ISA_na(query_bsp->mol);
+    }
+    if (seq_2  != NULL) {
+        sep = FastaToSeqBuff(seq_2, &sq_2, !is_aa2);
+        subject_bsp = (BioseqPtr) sep->data.ptrvalue;
+        is_na2 = FastaCheckDna(seq_2);
+    } else if (two != NULL && *two != NULLB) {
+       if (rid && database) {
+          /* Fetch the subject seqience from the BLAST database by the 
+             SeqId provided in the link */
+          sip = SeqIdParse(two);
+          ReadDBBioseqFetchEnable("wblast2", database, TRUE, TRUE);
+          subject_bsp = BioseqLockById(sip);
+          ReadDBBioseqFetchDisable();
+          if (!subject_bsp) {
+             error_msg = "The database sequence is not found";
+             Blast2SeqMainPage(error_msg, seq_1, seq_2, 
+                               one, two, NULL, is_prot, options, mtrx,
+                               from, to, ffrom, tto, filter, pagecount);
+          }
+       } else {
+          subject_bsp = FindSeqByAccession(two, 2, !is_aa2);
+       }
+       if (subject_bsp == NULL) {
+            error_msg = "The second sequence accession is not found";
+            Blast2SeqMainPage(error_msg, seq_1, seq_2, 
+                              one, two, NULL, is_prot, options, mtrx,
+                              from, to, ffrom, tto, filter, pagecount);
+        }
+        is_na2 = ISA_na(subject_bsp->mol);
+    }
+    code1 = ((is_aa1 == FALSE) ? Seq_code_iupacna:Seq_code_iupacaa);
+    code2 = ((is_aa2 == FALSE) ? Seq_code_iupacna:Seq_code_iupacaa);
+    
+    if (is_prot) {
+        if((chptr = WWWGetValueByName(theInfo->info, "MATRIX")) == NULL ||
+           *chptr == NULLB)
+            chptr = WWWGetValueByName(theInfo->info, "MTRX");
+        if (chptr && *chptr != NULLB)
+            mtrx = atoi(chptr);
+        else
+           mtrx = 0;
+        
+        switch(mtrx) {
+        case 1:
+           sprintf(mbuf, "PAM30");
+           if (gopen == -1 || gext == -1) {
+              gopen = (gopen == -1) ? 9: gopen;
+              gext = (gext == -1) ? 1: gext;
+           }
+           break;
+        case 2:
+           sprintf(mbuf, "PAM70");
+           if (gopen == -1 || gext == -1) {
+              gopen = (gopen == -1) ? 10: gopen;
+              gext = (gext == -1) ? 1: gext;
+           }
+           break;
+        case 3:
+           sprintf(mbuf, "PAM250");
+           if (gopen == -1 || gext == -1) {
+              gopen = (gopen == -1) ? 14: gopen;
+              gext = (gext == -1) ? 2: gext;
+           }
+           break;
+        case 4:
+           sprintf(mbuf, "BLOSUM90");
+           if (gopen == -1 || gext == -1) {
+              gopen = (gopen == -1) ? 10: gopen;
+              gext = (gext == -1) ? 1: gext;
+           }
+           break;
+        case 5:
+           sprintf(mbuf, "BLOSUM50");
+           if (gopen == -1 || gext == -1) {
+              gopen = (gopen == -1) ? 13: gopen;
+              gext = (gext == -1) ? 2: gext;
+           }
+           break;
+        default:
+           sprintf(mbuf, "BLOSUM62");
+           if (gopen == -1 || gext == -1) {
+              gopen = (gopen == -1) ? 11: gopen;
+              gext = (gext == -1) ? 1: gext;
+           }
+           break;
+        }
+
+        StringCpy(options->matrix, mbuf);
+        
+        /* one-pass non-multiple hits search with low threshold */		
+        options->two_pass_method  = FALSE;                      			
+        options->multiple_hits_only  = FALSE;
+        options->threshold_second = 9;
+    } else {
+        if (gopen == -1) 
+            gopen = (is_megablast) ? 0 : 5;
+        if (gext == -1) 
+            gext = (is_megablast) ? 0 : 2;
+        options->penalty  = ms;
+        options->reward  = ma;
+    }
+    
+    if ((chptr = WWWGetValueByName(theInfo->info, "DBLEN")) != NULL) {
+       options->db_length = atoi(chptr);
+    } else {
+       if((chptr = WWWGetValueByName(theInfo->info, "DB")) != NULL && 
+          StrCmp(chptr, "=pdb") == 0) {
+          dbname = StringSave("pdb");
+       } else {
+          dbname = StringSave("nr");
+       }
+    
+       rdfp = readdb_new(dbname, is_aa2);
+       if (rdfp) {
+          readdb_get_totals_ex(rdfp, &options->db_length, &dbseq_num, TRUE);
+          readdb_destruct(rdfp);
+       } else
+          options->db_length = (is_aa2 ? NR_SIZE_AA : NR_SIZE_NA);
+       
+       MemFree(dbname);
+    }
+
+    options->wordsize  = wordsize;
+    if (is_megablast) {
+        options->cutoff_s2 = options->wordsize*options->reward;
+        options->cutoff_s = (options->wordsize + 4)*options->reward;
+    }
+    options->gap_open  = gopen;
+    options->gap_extend  = gext;
+    options->gap_x_dropoff  = dropoff;
+    options->expect_value = expect;
+    options->filter = filter;
+    if (filter == 1) {
+        options->filter_string = StringSave("T");
+    }
+    
+    if (!StringICmp(progname, "tblastn") || 
+        !(StringICmp(progname, "tblastx")))
+        options->db_genetic_code = 1;
+    
+    if (query_bsp == NULL || subject_bsp == NULL) {
+        error_msg = "Please enter the sequences";   
+        Blast2SeqMainPage(error_msg, seq_1, seq_2, 
+                          one, two, NULL, is_prot, options, mtrx,
+                          from, to, ffrom, tto, filter, pagecount);
+    }
+    
+    error_return = NULL;
+    if (is_aa1 && is_na1) 
+        BlastConstructErrorMessage(NULL, "First sequence must be protein for this program", 1, &error_return);  
+    if (is_aa2 && is_na2)
+        BlastConstructErrorMessage(NULL, "Second sequence must be protein for this program", 1, &error_return);  
+    if (!is_aa1 && !is_na1)
+        BlastConstructErrorMessage(NULL, "First sequence must be nucleotide for this program", 1, &error_return);  
+    if (!is_aa2 && !is_na2)
+        BlastConstructErrorMessage(NULL, "Second sequence must be nucleotide for this program", 1, &error_return);  
+    if (error_return)
+        Blast2SeqMainPage(NULL, seq_1, seq_2, one, two, error_return, is_prot, 
+                          options, mtrx, from, to, ffrom, tto, filter, pagecount);
+    
+    BLASTOptionValidateHTML(options, progname, seq_1, seq_2, one, two, 
+                            is_prot, mtrx, from, to, ffrom, tto, filter,
+                            pagecount);
+
+    fake_bsp = BlastMakeFakeBioseq(query_bsp, NULL);
+    if (from == 0 && to == 0) {
+        ValNodeAddPointer(&slp1, SEQLOC_WHOLE, SeqIdDup(fake_bsp->id));
+        len1 = fake_bsp->length;
+    } else {
+        sip1 = SeqIntNew();
+        sip1->from = (from > 0) ? from-1 : 0; 
+        sip1->to = (to < fake_bsp->length) ? to-1 : fake_bsp->length-1;
+        sip1->id = (SeqIdPtr) SeqIdDup (fake_bsp->id);
+        sip1->strand = options->strand_option;
+        ValNodeAddPointer(&slp1, SEQLOC_INT, sip1);
+        len1 = SeqLocLen(slp1);
+    }
+    if (ffrom == 0 && tto == 0) {
+        ValNodeAddPointer(&slp2, SEQLOC_WHOLE,
+                          SeqIdDup(SeqIdFindBest(subject_bsp->id, SEQID_GI)));
+        len2 = subject_bsp->length;
+    } else {
+        sip2 = SeqIntNew();
+        sip2->from = (ffrom > 0) ? ffrom-1 : 0; 
+        sip2->to = (tto < subject_bsp->length) ? tto-1 : subject_bsp->length-1;
+        sip2->id = (SeqIdPtr) SeqIdDup(SeqIdFindBest(subject_bsp->id, SEQID_GI));
+        sip2->strand = Seq_strand_both;
+        ValNodeAddPointer(&slp2, SEQLOC_INT, sip2);
+        len2 = SeqLocLen(slp2);
+    }
+    if ((spp = SeqPortNewByLoc(slp1, code1)) == NULL) {
+        error_msg = "The first sequence location is not valid";
+        Blast2SeqMainPage(error_msg, seq_1, seq_2, one, two, NULL, is_prot, options, 
+                          mtrx, from, to, ffrom, tto, filter, pagecount);
+    } else
+       SeqPortFree(spp);
+    if ((spp = SeqPortNewByLoc(slp2, code2)) == NULL) {
+        error_msg = "The second sequence location is not valid";
+        Blast2SeqMainPage(error_msg, seq_1, seq_2, one, two, NULL, is_prot, options, 
+                          mtrx, from, to, ffrom, tto, filter, pagecount);
+    } else
+       SeqPortFree(spp);
+    
+    other_returns = NULL;
+
+#ifndef BL2SEQ_STANDALONE
+    loginfo.filename = StringSave("Log/wblast2.log");
+    loginfo.time_start = 0;
+    if (((loginfo.user_IP = getenv("PROXIED_IP")) == NULL) &&
+        ((loginfo.user_IP = getenv("USER_ADDR")) == NULL)) {
+       loginfo.user_IP = StringSave("255.255.255.255");
+    }
+    loginfo.pid = getpid();
+    loginfo.q_length = len1;
+    loginfo.s_length = len2;
+    loginfo.size = 0;
+
+    if (!is_megablast)
+       loginfo.program = StringSave(progname);
+    else
+       loginfo.program = StringSave("mblastn");
+    logmsg(0);
+#endif
+
+    seqalign =  BlastTwoSequencesByLocEx(slp1, slp2, progname, 
+                                         options, &other_returns, NULL);
+
+    run_status = WBLAST2_FORMAT;    
+    /*	seqalign =  BlastTwoSequencesEx(query_bsp, subject_bsp, progname, 
+        options, &other_returns, NULL);*/
+    
+    if (seqalign == NULL) {
+        if ((chptr = WWWGetValueByName(theInfo->info, "SEQ")) != NULL) {
+            MemFree(seq_1);
+            seq_1 = StringSave(chptr);
+        }
+        if((chptr = WWWGetValueByName(theInfo->info, "SSEQ")) != NULL) {
+            MemFree(seq_2);
+            seq_2 = StringSave(chptr);
+        }
+        CreateJavaHeadHTML(query_bsp, subject_bsp, from, to, ffrom, tto, 
+                           len1, len2, progname);
+        PrintParam(is_prot, mtrx, ma, ms, options, seq_2, seq_1, one, two,
+                   query_bsp, subject_bsp, len1, len2, from, to, ffrom, tto, pagecount);
+        printf("<strong><font color=#0000EE>No significant similarity was found</font></strong>\n");
+        MemFree(seq_1);
+        MemFree(seq_2);
+#ifndef BL2SEQ_STANDALONE
+        run_status = WBLAST2_DONE;
+        NlmThreadJoin(connection_thread, &thrstat);
+        logmsg(0);
+#endif
+        return 0;
+    }
+
+    mask = NULL;
+    for (vnp=other_returns; vnp; vnp = vnp->next) {
+        switch (vnp->choice) {
+           case TXDBINFO:
+               dbinfo = vnp->data.ptrvalue;
+               break;
+        case TXKABLK_NOGAP:
+            ka_params = vnp->data.ptrvalue;
+            break;
+        case TXKABLK_GAP:
+            ka_gap_params = vnp->data.ptrvalue;
+            break;
+        case TXPARAMETERS:
+            buffer = vnp->data.ptrvalue;
+            break;
+        case TXMATRIX:
+            blast_matrix = vnp->data.ptrvalue;
+            if (blast_matrix)
+                txmatrix = BlastMatrixToTxMatrix(blast_matrix);
+            break;
+        case SEQLOC_MASKING_NOTSET:
+        case SEQLOC_MASKING_PLUS1:
+        case SEQLOC_MASKING_PLUS2:
+        case SEQLOC_MASKING_PLUS3:
+        case SEQLOC_MASKING_MINUS1:
+        case SEQLOC_MASKING_MINUS2:
+        case SEQLOC_MASKING_MINUS3:
+            ValNodeAddPointer(&mask, vnp->choice, vnp->data.ptrvalue);
+            break;
+        default:
+            break;
+        }
+    }	
+    
+    ValNodeFree(other_returns);
+    
+    to = (to >0) ? to : fake_bsp->length;
+    tto = (tto >0) ? tto : subject_bsp->length;
+    from = (from >0) ? from : 1;
+    ffrom = (ffrom >0) ? ffrom : 1;
+    
+    CreateJavaHeadHTML(query_bsp, subject_bsp, 
+                       from, to, ffrom, tto, len1, len2, progname);
+    PrintParam(is_prot, mtrx, ma, ms, options, seq_2, seq_1, one, two,
+               query_bsp, subject_bsp, len1, len2, from, to, ffrom, tto, pagecount);
+    
+    MemFree(seq_1);
+    MemFree(seq_2);
+    align_type = BlastGetProgramNumber(progname);
+    
+    x_factor = y_factor = 1;
+    if (align_type == blast_type_tblastn)
+        x_factor = 3;
+    else if (align_type == blast_type_blastx)
+        y_factor = 3;
+    
+    x = y = 150;
+    ll = MAX(len1*x_factor, len2*y_factor);
+    scalex = (FloatHi) x*x_factor/ll;
+    scaley = (FloatHi) y*y_factor/ll;
+    k = 0;
+    color = 1;
+    index = 0;
+    
+    printf("<table>\n");
+    printf("<tr><td>\n");
+    
+    /* For tblastx all alignments are in one seqalign; let's separate them */
+    if (align_type == blast_type_tblastx) {
+       StdSegPtr nextssp;
+       SeqAlignPtr last_sap = NULL, head = NULL;
+       sap = seqalign;
+       ssp = seqalign->segs;
+       while (ssp) {
+          nextssp = ssp->next;
+          ssp->next = NULL;
+          seqalign->segs = ssp;
+          sap = SeqAlignDup(seqalign);
+          if (last_sap) {
+             last_sap->next = sap;
+             last_sap = last_sap->next;
+          } else
+             head = last_sap = sap;
+          ssp = nextssp;
+       }
+       SeqAlignFree(seqalign);
+       seqalign = head;
+    }
+
+    for (sap=seqalign; sap != NULL; sap = sap->next) {
+        if (sap->segtype > 3) {	
+            sap = sap->segs;
+        }
+        if (index%2 == 0) {
+            color = 1;
+        } else {
+            color = 2;
+        }
+        if (sap->segtype == SAS_DENDIAG) {
+            for (ddp = sap->segs, index1=0; ddp; ddp= ddp->next, index1++);
+        } else if (sap->segtype == SAS_DENSEG) {
+            dsp = sap->segs;
+            index1 = dsp->numseg;
+        } else if (sap->segtype == SAS_STD) {
+            for (ssp = sap->segs, index1=0; ssp; ssp = ssp->next, index1++);
+        }
+        
+        rect = MemNew((2*index1+3)*sizeof(PrymPtr));
+        rectY = MemNew((2*index1+3)*sizeof(PrymPtr));
+        k = CreateRectAlign(sap, rect, rectY, scalex, scaley,
+                            len1, len2, color, from, ffrom, to, tto);
+        DrawRectAlign(rect, k, color, 9, index);
+        /*	PrintRectAlign(rect, k, color, 9, index);*/
+        printf("<BR>\n");
+        DrawRectAlign(rectY, k, color, 9, index);
+        
+        MemFree(rect);
+        MemFree(rectY);
+        /*	PrintRectAlign(rectY, k, color, 9, index);*/
+        printf("<BR><BR>\n"); 
+        index++;
+    }
+    printf("</td><td width=75></td><td valign=top><b>2</b></td><td>\n");
+    xx = yy = 150;
+    scalex = ((FloatHi) xx) / len1;
+    scaley = ((FloatHi) yy) / len2;
+    
+    /*	printf("<INPUT TYPE=image border=0 SRC=\"bag?");*/
+    printf("<IMG border=0 SRC=\"bl2bag.cgi?");
+    xx = scalex * len1;
+    yy = scaley * len2;
+    printf("%s", NumToGun(xx));
+    printf("%s", NumToGun(yy));
+    printf("CCCCCC-");
+    
+    printf("rD9D9D9(");
+    
+    for (slp=qslp; slp != NULL; slp=slp->next) {
+        if (slp->choice == SEQLOC_PACKED_INT) {
+            for (sl = slp->data.ptrvalue; sl; sl=sl->next) {
+                if (SeqLocStart(sl) >= from || SeqLocStop(sl) <= to) {
+                    continue;
+                }
+                x = SeqLocStart(sl) * scalex;
+                printf("%s", NumToGun(x));
+                printf("00");
+                y = SeqLocStop(sl) * scaley;
+                printf("%s", NumToGun(x));
+                printf("%s", NumToGun(y));
+            }
+        } else {
+            if (SeqLocStart(slp) >= from || SeqLocStop(slp) <= to) {
+                continue;
+            }
+            x = SeqLocStart(slp) * scalex;
+            printf("%s", NumToGun(x));
+            printf("00");
+            y = SeqLocStop(slp) * scaley;
+            printf("%s", NumToGun(x));
+            printf("%s", NumToGun(y));
+        }
+    }
+    printf(")");
+    
+    hsat = NULL;
+    index = 0;
+    
+    for (sap=seqalign; sap != NULL; sap = sapnext) {
+        if (sap->segtype > 3) {	
+            sap = sap->segs;
+        }
+        sapnext = sap->next;
+        sap->next = NULL;
+        sat = SeqAnnotNew();
+        sat->type = 2;
+        sat->data = sap;
+        hsat = tie_next_annot(hsat, sat);
+        
+        if (index%2 == 0) {
+            printf("3399CC3(");
+        } else {
+            printf("8dC7CC3(");
+        }
+        if (sap->segtype == SAS_DENDIAG) {
+            ddp = sap->segs;
+            while (ddp != NULL) {
+                if (ddp->strands[0] != Seq_strand_minus) {
+                    x = ddp->starts [0] * scalex;
+                } else {
+                    x = (ddp->starts [0] + ddp->len) * scalex;
+                }
+                if (ddp->strands[1] != Seq_strand_minus) {
+                    y = yy - ddp->starts [1] * scaley;
+                } else {
+                    y = yy - (ddp->starts [1] + ddp->len) * scaley;
+                }
+                printf("%s", NumToGun(x));
+                printf("%s", NumToGun(y));
+                if (ddp->strands[0] != Seq_strand_minus) {
+                    x = (ddp->starts [0] + ddp->len) * scalex;
+                } else {
+                    x = ddp->starts [0] * scalex;
+                }
+                if (ddp->strands[1] != Seq_strand_minus) {
+                    y = yy - (ddp->starts [1] + ddp->len) * scaley;
+                } else {
+                    y = yy - ddp->starts [1] * scaley;
+                }
+                printf("%s", NumToGun(x));
+                printf("%s", NumToGun(y));
+                ddp = ddp->next;
+            }
+            printf(")");
+        } else if (sap->segtype == SAS_DENSEG) {
+            dsp = sap->segs;
+            for (index1=0; index1 < dsp->numseg; index1++) {
+                i2 = 2 * index1;
+                if (dsp->starts[i2] != -1 && dsp->starts[i2+1] != -1) {
+                    if (dsp->strands[i2] != Seq_strand_minus) {
+                        x = (dsp->starts[i2] - from) * scalex;
+                    } else {
+                        x = (dsp->starts[i2] + dsp->lens[index1] - from) * scalex;
+                    }
+                    if (dsp->strands[i2+1] != Seq_strand_minus) {
+                        y = yy - (dsp->starts[i2+1] -ffrom) * scaley;
+                    } else {
+                        y = yy - (dsp->starts[i2+1] + dsp->lens[index1] - ffrom) * scaley;
+                    }
+                    printf("%s", NumToGun(x));
+                    printf("%s", NumToGun(y));
+                    if (dsp->strands[i2] != Seq_strand_minus) {
+                        x = (dsp->starts[i2] + dsp->lens[index1] - from) * scalex;
+                    } else {
+                        x = (dsp->starts[i2] - from) * scalex;
+                    }
+                    if (dsp->strands[i2+1] != Seq_strand_minus) {
+                        y = yy - (dsp->starts[i2+1] + dsp->lens[index1] - ffrom) * scaley;
+                    } else {
+                        y = yy - (dsp->starts[i2+1] - ffrom)* scaley;
+                    }
+                    printf("%s", NumToGun(x));
+                    printf("%s", NumToGun(y));
+                }
+            }
+            printf(")");
+        } else if (sap->segtype == SAS_STD) {
+            SeqLocPtr tmp_slp;
+            ssp = sap->segs;
+            while (ssp) {
+                tmp_slp = ssp->loc;
+                if (!tmp_slp || !tmp_slp->next) {
+                    ssp = ssp->next;
+                    continue;
+                }
+                if (tmp_slp->choice != SEQLOC_EMPTY && 
+                    tmp_slp->next->choice != SEQLOC_EMPTY) {
+                    
+                    if (SeqLocStrand(tmp_slp) != Seq_strand_minus) {
+                        x = (SeqLocStart(tmp_slp) - from) * scalex;
+                    } else {
+                        x = (SeqLocStop(tmp_slp) + 1 - from) * scalex;
+                    }
+                    if (SeqLocStrand(tmp_slp->next) != Seq_strand_minus) {
+                        y = yy - (SeqLocStart(tmp_slp->next) - ffrom) * scaley;
+                    } else {
+                        y = yy - (SeqLocStop(tmp_slp->next) + 1 - ffrom) * scaley;
+                    }
+                    printf("%s", NumToGun(x));
+                    printf("%s", NumToGun(y));
+                    if (SeqLocStrand(tmp_slp) != Seq_strand_minus) {
+                        x = (SeqLocStop(tmp_slp) + 1 - from) * scalex;
+                    } else {
+                        x = (SeqLocStart(tmp_slp) - from) * scalex;
+                    }
+                    if (SeqLocStrand(tmp_slp->next) != Seq_strand_minus) {
+                        y = yy - (SeqLocStop(tmp_slp->next) + 1 - ffrom) * scaley;
+                    } else {
+                        y = yy - (SeqLocStart(tmp_slp->next) - ffrom) * scaley;
+                    }
+                    printf("%s", NumToGun(x));
+                    printf("%s", NumToGun(y));
+                }
+                ssp = ssp->next;
+            }
+            printf(")");
+        }
+        
+        index++;
+    }
+
+#ifndef BL2SEQ_STANDALONE
+    loginfo.size = index;
+#endif
+
+    printf("\">\n");
+    printf("</td><td valign=bottom><b>1</b></td></tr></table>\n");
+    printf("<BR>");
+    
+    color = 1;
+    index = 0;
+    printf("<font color=#FF0000>NOTE:</font>The statistics (bitscore and expect value) is calculated based on the size of nr database<BR><BR>\n");
+    
+    if (align_type == blast_type_blastn)
+       printf("<font color=#FF0000>NOTE:</font>If protein translation is reversed, please repeat the search with reverse strand of the query sequence<BR><BR>\n");
+
+    for (sat=hsat; sat != NULL; sat=satnext) {
+        satnext=sat->next;
+        sat->next = NULL;
+        
+        x = y = 450;
+        
+        ll = MAX(len1*x_factor, len2*y_factor);
+        scalex = (FloatHi) x*x_factor/ll;
+        scaley = (FloatHi) y*y_factor/ll;
+        k = 0;
+        
+        if ((sap = sat->data) != NULL) {
+            if (index%2 == 0) {
+                color = 1;
+            } else {
+                color = 2;
+            }
+            printf("<a name=%d>\n", index);
+            PrintOutScore(sap, is_prot, NULL, mask);
+            if (sap->segtype == SAS_DENDIAG) {
+                for (ddp = sap->segs, index1=0; ddp; ddp= ddp->next, index1++);
+            } else if (sap->segtype == SAS_DENSEG) {
+                dsp = sap->segs;
+                index1 = dsp->numseg;
+            } else if (sap->segtype == SAS_STD) {
+                ssp = sap->segs;
+                for (ssp = sap->segs, index1=0; ssp; ssp= ssp->next, index1++);
+            }
+            rect = MemNew((2*index1+3)*sizeof(PrymPtr));
+            rectY = MemNew((2*index1+3)*sizeof(PrymPtr));
+            
+            k = CreateRectAlign(sap, rect, rectY, scalex, scaley,
+                                len1, len2, color, from, ffrom, to, tto);
+            DrawRectAlign(rect, k, color, 11, -1);
+            MemFree(rect);
+            printf("<BR>\n");
+            DrawRectAlign(rectY, k, color, 11, -1);
+            MemFree(rectY);
+            printf("<BR><BR>\n");
+            index++;
+        }
+           
+        txoption = 0;
+        txoption += TXALIGN_COMPRESS;
+        txoption += TXALIGN_END_NUM;
+        txoption += TXALIGN_SHOW_GI;
+        txoption += TXALIGN_MATRIX_VAL;
+        txoption += TXALIGN_SHOW_QS;
+           
+        if (StringICmp(progname, "blastx") == 0)
+            txoption += TXALIGN_BLASTX_SPECIAL;
+        
+        txoption += TXALIGN_HTML;
+        
+        AddAlignInfoToSeqAnnot(sat, align_type); 
+        
+        ShowTextAlignFromAnnot(sat, 60, stdout, NULL, NULL,
+                               txoption, txmatrix, mask, NULL);
+    }
+
+    SeqLocSetFree(slp1);
+    SeqLocSetFree(slp2);
+    if (one && *one != NULLB)
+       BioseqUnlock(query_bsp);
+    else
+       BioseqFree(query_bsp);
+    if (two && *two != NULLB)
+       BioseqUnlock(subject_bsp);
+    else
+       BioseqFree(subject_bsp);
+
+    BlastTimeFillStructure(&time_keeper);
+    printf("<pre>\n");
+    fprintf(stdout, "CPU time: %8.2f user secs.\t%8.2f sys. "
+            "secs\t%8.2f total secs.\n\n", 
+            time_keeper.user, time_keeper.system, time_keeper.total);
+    init_buff();
+    /*PrintDbReport(dbinfo, 70, stdout);*/
+    
+    blast_matrix = BLAST_MatrixDestruct(blast_matrix);
+    if (txmatrix)
+        txmatrix = TxMatrixDestruct(txmatrix);
+    dbinfo = TxDfDbInfoDestruct(dbinfo);
+    if (ka_params) {
+        PrintKAParameters(ka_params->Lambda, ka_params->K, ka_params->H, 
+                          70, stdout, FALSE);
+        MemFree(ka_params);
+    }
+    if (ka_gap_params) {
+        PrintKAParameters(ka_gap_params->Lambda, ka_gap_params->K, 
+                          ka_gap_params->H, 70, stdout, TRUE);
+        MemFree(ka_gap_params);
+    }
+    PrintTildeSepLines(buffer, 70, stdout);
+    MemFree(buffer);
+    free_buff();
+    mask_head = mask;
+    while (mask) {
+        SeqLocSetFree(mask->data.ptrvalue);
+        mask = mask->next;
+    }
+    ValNodeFree(mask_head);
+    CreateTailHTML();
+    run_status = WBLAST2_DONE;
+    options = BLASTOptionDelete(options);
+    WWWInfoFree(theInfo->info);
+    MemFree(progname);
+    MemFree(theInfo);
+#ifndef BL2SEQ_STANDALONE 
+    /* Connection thread not spawned for the WWW server version */
+    NlmThreadJoin(connection_thread, &thrstat);
+    logmsg(0);
+    LogInfoFree();
+#endif
+    return 0;
+}
diff --git a/network/wwwblast/Src/wwwblast.c b/network/wwwblast/Src/wwwblast.c
new file mode 100644
index 00000000..9582e926
--- /dev/null
+++ b/network/wwwblast/Src/wwwblast.c
@@ -0,0 +1,1275 @@
+/* $Id: wwwblast.c,v 1.8 2003/06/04 16:12:51 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: wwwblast.c,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Creation Date: 03/15/2000
+*
+* $Revision: 1.8 $
+*
+* File Description:
+*        Standalone WWW Blast CGI program.
+*
+* $Log: wwwblast.c,v $
+* Revision 1.8  2003/06/04 16:12:51  dondosha
+* Set db genetic code for formatting
+*
+* Revision 1.7  2003/05/13 22:00:37  dondosha
+* More changes to make alternative links work
+*
+* Revision 1.6  2003/05/13 21:17:01  dondosha
+* Pass www_blast_type to txalign in all cases
+*
+* Revision 1.5  2003/05/09 21:09:05  dondosha
+* Removed unused variables
+*
+* Revision 1.4  2003/05/02 23:04:03  dondosha
+* Fixed paths for non-standard setups, removed blast_form.map
+*
+* Revision 1.3  2003/04/29 15:55:56  dondosha
+* Always use root path in links
+*
+* Revision 1.2  2003/02/10 21:48:53  dondosha
+* Added support for multi-query XML output
+*
+* Revision 1.1  2002/12/02 18:05:53  dondosha
+* Moved from different locations to a common one
+*
+* Revision 6.32  2002/06/19 22:50:17  dondosha
+* Added all queries information for tabular output with multiple queries
+*
+* Revision 6.31  2002/06/18 21:14:28  dondosha
+* Added return statement in the end of AppendMegaBlastHit
+*
+* Revision 6.30  2002/01/08 22:36:25  dondosha
+* Added tabular output functionality
+*
+* Revision 6.29  2000/11/29 16:11:31  dondosha
+* If multiple queries, send proper lower case mask to the search engine
+*
+* Revision 6.28  2000/11/17 14:40:04  dondosha
+* Changed MegaBlastResultsNew call to MemNew
+*
+* Revision 6.27  2000/11/16 22:37:07  dondosha
+* Added endpoint Mega BLAST results handling
+*
+* Revision 6.26  2000/10/31 20:18:52  shavirin
+* Added printing of correct XML output when no hits found
+* Added printing progeress messages to avoid browser timeout.
+*
+* Revision 6.25  2000/10/23 20:19:57  dondosha
+* Open and close AsnIo outside calls to BXMLPrintOutput function
+*
+* Revision 6.24  2000/10/18 20:19:31  shavirin
+* Added title for OOF Blastx.
+*
+* Revision 6.23  2000/10/16 22:18:17  shavirin
+* Added possibility to perform OOF blastx
+*
+* Revision 6.22  2000/10/16 20:27:03  shavirin
+* Added possibility to run RPS Blast.
+*
+* Revision 6.21  2000/09/28 16:48:20  dondosha
+* Changed MegaBlast related code to get a single SeqAlignPtr from server
+*
+* Revision 6.20  2000/09/28 15:16:55  shavirin
+* Added message if request was limited to results of Entrez query.
+*
+* Revision 6.19  2000/09/27 22:17:04  shavirin
+* Added possibility to limit search to results of entrez query.
+*
+* Revision 6.18  2000/09/13 22:28:10  dondosha
+* Removed extra </PRE> that is now printed in PrintDefLinesFromSeqAlign
+*
+* Revision 6.17  2000/09/13 20:47:51  dondosha
+* Small cleanup with closures of html blocks
+*
+* Revision 6.16  2000/09/12 21:57:28  dondosha
+* Pass the correct scoring matrix to ShowTextAlignFromAnnot
+*
+* Revision 6.15  2000/09/11 17:51:07  shavirin
+* Removed redundant <PRE> tag.
+*
+* Revision 6.14  2000/09/08 20:18:12  dondosha
+* Print the title, background and GIF image before creating options
+*
+* Revision 6.13  2000/09/08 14:49:28  dondosha
+* Allow graphical overview with multiple queries
+*
+* Revision 6.12  2000/09/07 18:01:38  dondosha
+* Pass a callback to the server from TraditionalBlastReportEngineWithImage; allow multiple queries for all BLAST searches
+*
+* Revision 6.11  2000/09/05 18:00:25  dondosha
+* Added query acknowledgement for each query in WWWBlastDoSearch for megablast
+*
+* Revision 6.10  2000/09/01 17:55:14  dondosha
+* Call SeqEntryLoad at the beginning; corrections for megablast page
+*
+* Revision 6.9  2000/08/30 22:22:35  dondosha
+* Enhance function WWWBlastDoSearch to handle megablast search
+*
+* Revision 6.8  2000/08/28 20:20:59  dondosha
+* Added functionality for megablast web page
+*
+* Revision 6.7  2000/08/09 20:30:30  shavirin
+* Added possibility to print XML output.
+*
+* Revision 6.6  2000/07/31 20:44:12  shavirin
+* Minor change (initialized variable) from Haruna Cofer (haruna@detroit.sgi.com)
+*
+* Revision 6.5  2000/05/17 15:50:51  shavirin
+* Moved many functions to the wwwbutl.c file.
+*
+* Revision 6.4  2000/04/21 18:10:59  shavirin
+* Added possibility to print Patrick's alignment.
+*
+* Revision 6.3  2000/03/28 14:44:20  shavirin
+* Changed function ctime_r to ctime() for compatibility.
+*
+* Revision 6.2  2000/03/24 16:05:37  shavirin
+* Added option to be used as NCBI client/server.
+*
+* Revision 6.1  2000/03/20 19:01:00  shavirin
+* Initial revision.
+*
+*
+* ==========================================================================
+*/
+
+#include <wwwblast.h>
+#include <xmlblast.h>
+
+static int LIBCALLBACK WWWTickCallback(Int4 sequence_number, 
+                                       Int4 number_of_positive_hits)
+{
+    if(!TestSTDOut()) {
+	return -1;
+    }
+    
+    /*    fprintf(stdout, "."); */
+
+    printf("<!-- Progress msg from the server %d %d-->\n", 
+           sequence_number, number_of_positive_hits);
+
+    fflush(stdout);
+    
+    return 1;
+}
+static Int4 get_number_alignment(SeqAlignPtr align)
+{
+    Int4 num = 0;
+
+    while(align)
+    {
+	++num;
+	align = align->next;
+    }
+
+    return num;
+}
+static void
+PrintMotd(CharPtr string, FILE *fp, Boolean html_format)
+
+{
+    Char buffer[100];
+    CharPtr ptr;
+    
+    if (string == NULL)
+        return;
+    
+    buffer[0] = NULLB;
+    ptr = buffer;
+    
+    if (html_format) {
+        fprintf(fp, "<PRE>\n");
+    }
+    
+    while (*string != NULLB) {
+        if (*string == '~') {
+            *ptr = NULLB;
+            fprintf(fp, "%s\n", buffer);
+            buffer[0] = NULLB;
+            ptr = buffer;
+            string++;
+            if (*string == NULLB)
+                break;
+        } else {
+            *ptr=*string;
+            ptr++;  string++;
+        }
+    }
+    *ptr = NULLB;
+    fprintf(fp, "%s\n", buffer);
+    
+    if (html_format) {
+        fprintf(fp, "</PRE>\n");
+    }
+    
+    fflush(fp);
+
+    return;
+}
+#ifdef NCBI_CLIENT_SERVER
+
+static  Boolean LIBCALLBACK
+callback (BlastResponsePtr brp, Boolean PNTR cancel)
+
+{
+        fprintf(stdout, "</PRE>\n<PRE>");
+	return TRUE;
+}
+
+static Boolean
+TraditionalBlastReportEngineWithImage(SeqLocPtr slp, BioseqPtr bsp, BlastNet3Hptr bl3hp, WWWBlastInfoPtr theInfo)
+
+{
+    BlastDbinfoPtr dbinfo;
+    BlastKABlkPtr ka_params=NULL, ka_params_gap=NULL;
+    BlastPruneSapStructPtr prune;
+    BLAST_MatrixPtr matrix;
+    Int4Ptr PNTR txmatrix;
+    Boolean query_is_na, db_is_na;
+    Boolean status;
+    CharPtr params_buffer=NULL;
+    Int4 number_of_hits_private=0, length;
+    SeqAlignPtr seqalign = NULL, sap, next_seqalign;
+    SeqAnnotPtr seqannot=NULL;
+    TxDfDbInfoPtr tx_dbinfo=NULL, tx_dbinfo_head;
+    ValNodePtr mask_loc, mask_loc_start, other_returns, error_returns, vnp, vnp1=NULL;
+    Uint1 align_type;
+    Uint1 f_order[FEATDEF_ANY], g_order[FEATDEF_ANY];
+    /* Variables for multiple query output */
+    SeqLocPtr tmp_slp;
+    Boolean done = TRUE;
+    BLAST_OptionsBlkPtr options = theInfo->options;
+    CharPtr program = theInfo->program, database = theInfo->database;
+    Uint4 align_options = theInfo->align_options;
+    DenseSegPtr dsp, next_dsp;
+    AsnIoPtr xml_aip;
+    MegaBlastResultsPtr mb_results = NULL;
+    Boolean tabular_output = (theInfo->align_view == HitTable || 
+                              theInfo->align_view == HitTableWithHeader);
+    
+    MemSet((Pointer)(g_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
+    MemSet((Pointer)(f_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
+    
+    if (bsp == NULL && slp == NULL)
+        return FALSE;
+    
+    if (bl3hp == NULL || program == NULL || database == NULL)
+        return FALSE;
+    
+    align_type = BlastGetTypes(program, &query_is_na, &db_is_na);
+    
+    init_buff_ex(85);
+    dbinfo = BlastRequestDbInfo(bl3hp, database, !db_is_na);
+    
+    if (dbinfo && !tabular_output && 
+        !(options->is_megablast_search && options->no_traceback))
+        PrintDbInformationBasic(database, !db_is_na, 70, dbinfo->definition, dbinfo->number_seqs, dbinfo->total_length, stdout, TRUE);
+    dbinfo = BlastDbinfoFree(dbinfo);
+    free_buff();
+    
+    if (bsp) 
+        seqalign = BlastBioseqNetCore(bl3hp, bsp, program, database, options, &other_returns, &error_returns, callback, NULL, &status);
+    else if (options->is_megablast_search) {
+        seqalign = MegaBlastSeqLocNetCore(bl3hp, slp, program, database, options, &other_returns, &error_returns, callback, &status);
+    } else
+        seqalign = BlastSeqLocNetCore(bl3hp, slp, program, database, options, &other_returns, &error_returns, callback, NULL, &status);
+    
+    
+    BlastErrorPrintExtra(error_returns, TRUE, stdout);
+    
+    mask_loc = NULL;
+    matrix = NULL;
+    txmatrix = NULL;
+    for (vnp=other_returns; vnp; vnp = vnp->next) {
+        switch (vnp->choice) {
+           case BlastResponse_mbalign:
+           mb_results = (MegaBlastResultsPtr) vnp->data.ptrvalue;
+           break;
+        case TXDBINFO:
+	    tx_dbinfo = (TxDfDbInfoPtr) vnp->data.ptrvalue;
+            break;
+        case TXKABLK_NOGAP:
+            ka_params = (BlastKABlkPtr) vnp->data.ptrvalue;
+            break;
+        case TXKABLK_GAP:
+	    ka_params_gap = (BlastKABlkPtr) vnp->data.ptrvalue;
+            break;
+        case TXPARAMETERS:
+	    params_buffer = (CharPtr) vnp->data.ptrvalue;
+            break;
+        case TXMATRIX:
+            matrix = (BLAST_MatrixPtr) vnp->data.ptrvalue;
+            if (matrix)
+                txmatrix = BlastMatrixToTxMatrix(matrix);
+            /*BLAST_MatrixDestruct(matrix);*/
+            break;
+        case SEQLOC_MASKING_NOTSET:
+        case SEQLOC_MASKING_PLUS1:
+        case SEQLOC_MASKING_PLUS2:
+        case SEQLOC_MASKING_PLUS3:
+        case SEQLOC_MASKING_MINUS1:
+        case SEQLOC_MASKING_MINUS2:
+        case SEQLOC_MASKING_MINUS3:
+	    if (!options->is_megablast_search)
+                ValNodeAddPointer(&mask_loc, vnp->choice, vnp->data.ptrvalue);
+	    break;
+        default:
+            break;
+        }
+    }	
+    
+    /* If results come as alignment endpoints only from Mega BLAST */
+    if (mb_results) {
+       MegaBlastHitPtr mb_hit = mb_results->mbhits, next_hit;
+
+       while (mb_hit) {
+          fprintf(stdout, "%s\t%s\t%d\t%d\t%d\t%d\t%d\n", mb_hit->id1,
+                  mb_hit->id2, mb_hit->query_offset, mb_hit->subject_offset,
+                  mb_hit->query_end, mb_hit->subject_end, mb_hit->score);
+          mb_hit = mb_hit->next;
+       }
+       MegaBlastResultsFree(mb_results);
+    } else if (!seqalign) {
+       done = FALSE;
+    }
+    
+    ReadDBBioseqFetchEnable ("blastall", database, db_is_na, TRUE);
+    ReadDBBioseqSetDbGeneticCode(theInfo->options->db_genetic_code);
+   
+    tmp_slp = slp;
+    
+    if(theInfo->xml_output)
+        xml_aip = AsnIoOpen("stdout", "wx");
+
+    if (tabular_output) {
+       if (theInfo->align_view == HitTableWithHeader)
+          PrintTabularOutputHeader(database, bsp, slp,
+              (options->is_megablast_search ? "megablast" : program),
+              0, FALSE, stdout);
+
+       BlastPrintTabulatedResults(seqalign, bsp, slp, 
+                                  theInfo->number_of_alignments,
+                                  program, 
+                                  !theInfo->options->gapped_calculation,
+                                  FALSE, SeqLocStart(slp), 0, stdout,
+                                  (theInfo->align_view == HitTableWithHeader));
+       SeqAlignSetFree(seqalign);
+    } else {
+    while (seqalign) {
+        if (!options->is_megablast_search)
+            next_seqalign = NULL;
+        else {
+            sap = seqalign;
+            while (sap != NULL) { 
+                if (sap->next != NULL) {
+                    dsp = (DenseSegPtr) (sap->segs);
+                    next_dsp = (DenseSegPtr) (sap->next->segs);
+                    
+                    if (SeqIdComp(dsp->ids, next_dsp->ids) != SIC_YES) {
+                        next_seqalign = sap->next;
+                        sap->next = NULL;
+                    }
+                } else
+                    next_seqalign = NULL;
+                sap = sap->next;
+            }
+            
+            dsp = (DenseSegPtr) (seqalign->segs);
+            while (tmp_slp && SeqIdComp(dsp->ids, SeqLocId(tmp_slp)) != SIC_YES)
+                tmp_slp = tmp_slp->next;
+            if (tmp_slp == NULL) /* Should never happen */
+                break;
+            bsp = BioseqLockById(SeqLocId(tmp_slp));
+            init_buff_ex(85);
+            fprintf(stdout, "<HR><BR>");
+            AcknowledgeBlastQuery(bsp, 70, stdout, FALSE, TRUE);
+            free_buff();
+            BioseqUnlock(bsp);
+        }
+        
+        if(theInfo->xml_output) {
+            printf("<PRE>");
+            BXMLPrintOutput(xml_aip, seqalign, options, 
+                            program, database, 
+                            bsp, other_returns, 0, NULL);
+            AsnIoReset(xml_aip);
+            printf("</PRE>");
+            
+        } else {
+            
+            seqannot = SeqAnnotNew();
+            seqannot->type = 2;
+            AddAlignInfoToSeqAnnot(seqannot, align_type);
+            seqannot->data = seqalign;
+            
+            if(theInfo->show_overview) {
+                Char f_name[64], title[1024], href[64];
+                Int4 align_num;       
+                
+                sprintf(f_name, "%ld%ld.gif", (long)random(), (long)getpid());
+                sprintf(href, "nph-viewgif.cgi?");
+                
+                align_num = get_number_alignment(seqalign); 
+                sprintf(title, 
+                        "<H3><a href=\"%s/blast/docs/newoptions.html#graphical-overview\"> "
+                        "Distribution of %ld Blast Hits on the Query Sequence</a> "
+                        "</H3>\n", theInfo->www_root_path, (long)align_num);
+                
+                /* Open HTML form */
+                fprintf(stdout, "<FORM NAME=\"BLASTFORM\">\n");
+                fflush(stdout);
+                
+                PrintAlignmentOverview(seqannot, stdout, 
+                                       "BLASTFORM", href, f_name, title); 
+            }
+            
+            prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_descriptions, NULL);
+            ObjMgrSetHold();
+            init_buff_ex(85);
+            
+            PrintDefLinesFromSeqAlignEx2(prune->sap, 80, stdout, theInfo->print_options, FIRST_PASS, NULL, theInfo->number_of_descriptions, database, theInfo->www_blast_type);
+            free_buff();
+            
+            prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_alignments, prune);
+            seqannot->data = prune->sap;
+            
+            if(theInfo->color_schema != 0 && 
+               (!StringICmp(program, "blastn") || 
+                !StringICmp(program, "blastp"))) {
+                
+                if(!DDV_DisplayBlastPairList(prune->sap, mask_loc, stdout, 
+                                             query_is_na, align_options, 
+                                             theInfo->color_schema)) { 
+                    fprintf(stdout, 
+                            "\n\n!!!\n   "
+                            "    --------  Failure to print alignment...  --------"
+                            "\n!!!\n\n");
+                    fflush(stdout);
+                }
+            } else {
+                
+                if(options->is_ooframe) {
+                    printf("<PRE>");
+                    OOFShowBlastAlignment(seqalign, /*mask*/ NULL,
+                                          stdout, align_options, txmatrix);
+                } else {
+                    if (align_options & TXALIGN_MASTER) {
+                        ShowTextAlignFromAnnot2(seqannot, 60, stdout, f_order,
+                           g_order, align_options, txmatrix, mask_loc, NULL, 
+                           NULL, theInfo->www_blast_type);
+                    } else {
+                        ShowTextAlignFromAnnot2(seqannot, 60, stdout, f_order, 
+                           g_order, align_options, txmatrix, mask_loc, 
+                           FormatScoreFunc, NULL, theInfo->www_blast_type);
+                    }
+                }
+            }
+            
+            seqannot->data = seqalign;
+            number_of_hits_private = prune->original_number; 
+            prune = BlastPruneSapStructDestruct(prune);
+            ObjMgrClearHold();
+            ObjMgrFreeCache(0);
+        } /* If else xml_output */
+        
+        if (options->is_megablast_search)
+            tmp_slp = tmp_slp->next;
+        if (seqannot)
+            seqannot = SeqAnnotFree(seqannot);
+        seqalign = next_seqalign;
+        fprintf(stdout, "<PRE>\n");
+    }
+    } /* End if not hit table */ 
+    if (!done) { /* seqalign == NULL */
+    if(theInfo->xml_output && !options->is_ooframe) {
+       BlastErrorMsgPtr error_msg;
+       CharPtr message;
+       
+       if (error_returns == NULL) {
+                message = "No hits found";
+       } else {
+          error_msg = error_returns->data.ptrvalue;
+          message = error_msg->msg;
+       }
+       
+       BXMLPrintOutput(xml_aip, NULL, 
+                       options, program, database, 
+                       bsp, other_returns, 0, message);
+       
+       if (error_returns != NULL) {
+          MemFree(error_msg->msg);
+          MemFree(error_msg);
+          MemFree(error_returns);
+       }
+       
+       AsnIoReset(xml_aip);
+    } else if (!tabular_output) {
+       fprintf(stdout, "\n\n ***** No hits found ******\n\n");
+    }
+    }
+    if(theInfo->xml_output)
+        xml_aip = AsnIoClose(xml_aip);
+    
+    BLAST_MatrixDestruct(matrix);
+    if (txmatrix)
+        txmatrix = TxMatrixDestruct(txmatrix);
+    
+    mask_loc_start = mask_loc;
+    while (mask_loc) {
+        SeqLocSetFree(mask_loc->data.ptrvalue);
+        mask_loc = mask_loc->next;
+    }
+    ValNodeFree(mask_loc_start);
+               
+    init_buff_ex(85);
+    tx_dbinfo_head = tx_dbinfo;
+    if (!tabular_output && 
+        !(options->is_megablast_search && options->no_traceback)) {
+        while (tx_dbinfo) {
+            PrintDbReport(tx_dbinfo, 70, stdout);
+            tx_dbinfo = tx_dbinfo->next;
+        }
+    }
+    tx_dbinfo_head = TxDfDbInfoDestruct(tx_dbinfo_head);
+    
+    if (ka_params) {
+        if (!tabular_output && 
+            !(options->is_megablast_search && options->no_traceback))
+            PrintKAParameters(ka_params->lambda, ka_params->k, ka_params->h, 
+                              70, stdout, FALSE);
+            MemFree(ka_params);
+    }
+    if (ka_params_gap) {
+        if (!tabular_output && 
+            !(options->is_megablast_search && options->no_traceback))
+            PrintKAParameters(ka_params_gap->lambda, ka_params_gap->k, ka_params_gap->h, 70, stdout, TRUE);
+        MemFree(ka_params_gap);
+    }
+    
+    if (!tabular_output && 
+        !(options->is_megablast_search && options->no_traceback))
+        PrintTildeSepLines(params_buffer, 70, stdout);
+    
+    printf("</PRE></BODY></HTML>\n");
+    MemFree(params_buffer);
+    free_buff();
+    
+    other_returns = ValNodeFree(other_returns);
+    
+    return status;
+}
+
+static Boolean
+TraditionalBlastReportWithImage(BioseqPtr bsp, BlastNet3Hptr bl3hp, 
+                                WWWBlastInfoPtr theInfo)
+{
+   return TraditionalBlastReportEngineWithImage(NULL, bsp, bl3hp, theInfo);
+}
+static Boolean
+TraditionalBlastReportLocWithImage(SeqLocPtr slp, BlastNet3Hptr bl3hp,
+                                   WWWBlastInfoPtr theInfo)
+{
+   return TraditionalBlastReportEngineWithImage(slp, NULL, bl3hp, theInfo);
+}
+
+Boolean WWWBlastDoClientSearch(WWWBlastInfoPtr theInfo)
+{
+    BlastNet3Hptr	bl3hp;
+    BlastResponsePtr	response;
+    BlastVersionPtr	blast_version;
+    CharPtr		date, motd, version;
+    Boolean status;
+    
+    if(theInfo == NULL)
+	return FALSE;
+        
+    if (!BlastInit("blastcl3", &bl3hp, &response)) {
+        WWWBlastErrMessage(BLASTErrClient, NULL);                
+        return FALSE;
+    }
+    
+    if (response && response->choice == BlastResponse_init) {
+        blast_version = response->data.ptrvalue;
+        version = blast_version->version;
+        date = blast_version->date;
+    } else {
+        WWWBlastErrMessage(BLASTErrClient, NULL);                
+        return FALSE;
+    }
+
+    BlastNetBioseqFetchEnable(bl3hp, theInfo->database, 
+                              theInfo->db_is_na, TRUE);
+    
+#ifdef BLAST_PRINT_MOTD
+    motd = Blast3GetMotd(bl3hp);
+    PrintMotd(motd, stdout, TRUE);
+    motd = MemFree(motd);
+#endif
+    
+    if (!theInfo->options->is_megablast_search)
+       status = TraditionalBlastReportWithImage(theInfo->fake_bsp, bl3hp, theInfo);
+    else 
+       status = TraditionalBlastReportLocWithImage(theInfo->query_slp, bl3hp, theInfo);
+    if (status == FALSE) {
+        WWWBlastErrMessage(BLASTErrServer, NULL);
+        return FALSE;
+    }
+    
+    return TRUE;
+}
+#endif
+
+#define BUFFER_LENGTH 255
+
+static int LIBCALLBACK
+AppendMegaBlastHit(VoidPtr ptr)
+{
+   BlastSearchBlkPtr search = (BlastSearchBlkPtr) ptr;
+   SeqIdPtr subject_id, query_id;
+   CharPtr subject_descr, subject_buffer;
+   Int4 index, query_length;
+   Int2 context;
+   BLAST_HSPPtr hsp;
+   MegaBlastResultsPtr mb_results;
+   MegaBlastHitPtr new_hit, last_hit = NULL;
+
+   if (search->current_hitlist == NULL || search->current_hitlist->hspcnt <= 0) {
+      search->subject_info = BLASTSubjectInfoDestruct(search->subject_info);
+      return 0;
+   }
+
+   mb_results = (MegaBlastResultsPtr)
+      search->mb_endpoint_results->data.ptrvalue;
+   if (mb_results) {
+       for (last_hit = mb_results->mbhits; last_hit->next; 
+            last_hit = last_hit->next);
+   }
+   readdb_get_descriptor(search->rdfp, search->subject_id, &subject_id,
+			 &subject_descr);
+   if (subject_id->choice != SEQID_GENERAL) {
+      subject_buffer = (CharPtr) Malloc(BUFFER_LENGTH + 1);
+      SeqIdWrite(SeqIdFindBestAccession(subject_id), subject_buffer,
+                 PRINTID_TEXTID_ACC_VER, BUFFER_LENGTH);
+   } else {
+      subject_buffer = StringTokMT(subject_descr, " ", &subject_descr);
+      subject_descr = subject_buffer;
+   }
+
+   for (index=0; index<search->current_hitlist->hspcnt; index++) {
+      hsp = search->current_hitlist->hsp_array[index];
+      if (hsp==NULL || (search->pbp->cutoff_e > 0 && 
+	  hsp->evalue > search->pbp->cutoff_e)) 
+	 continue;
+      new_hit = Malloc(sizeof(MegaBlastHit));
+      new_hit->next = NULL;
+      context = hsp->context; 
+      query_id = search->qid_array[context/2];
+
+      new_hit->id2 = StringSave(subject_buffer);
+      if (query_id->choice == SEQID_LOCAL) {
+         BioseqPtr query_bsp = BioseqLockById(query_id);
+         CharPtr title = StringSave(BioseqGetTitle(query_bsp));
+         if (title) {
+            new_hit->id1 = StringTokMT(title, " ", &title);
+         } else {
+            Int4 query_gi;
+            Boolean numeric_query_id =
+                GetAccessionFromSeqId(query_bsp->id, &query_gi,
+                                      &new_hit->id1);
+            if (numeric_query_id) {
+                new_hit->id1 = Malloc(10);
+                sprintf(new_hit->id1, "%d", query_gi);
+            }
+         }  
+         BioseqUnlock(query_bsp);
+      } else {
+          new_hit->id1 = (CharPtr) Malloc(BUFFER_LENGTH + 1);
+          SeqIdWrite(SeqIdFindBestAccession(query_id), new_hit->id1,
+                     PRINTID_TEXTID_ACC_VER, BUFFER_LENGTH);
+      }
+      query_length = search->query_context_offsets[context+1] -
+         search->query_context_offsets[context] - 1;
+      if (context & 1) {
+	 new_hit->query_end = query_length - hsp->query.offset;
+	 new_hit->query_offset = 
+	    new_hit->query_end - hsp->query.length + 1;
+      } else {
+         new_hit->query_offset = hsp->query.offset + 1;
+	 new_hit->query_end = new_hit->query_offset + hsp->query.length - 1;
+      }
+
+      new_hit->subject_offset = hsp->subject.offset + 1;
+      new_hit->subject_end = hsp->subject.end;
+      
+      if (search->pbp->gap_open==0 && search->pbp->gap_extend==0)
+	 new_hit->score = ((hsp->subject.length + hsp->query.length)*
+		   search->sbp->reward / 2 - hsp->score) / 
+	    (search->sbp->reward - search->sbp->penalty);
+      else 
+	 new_hit->score = hsp->score;
+      if (last_hit == NULL) {
+         last_hit = new_hit;
+         mb_results = MemNew(sizeof(MegaBlastResults));
+         mb_results->mbhits = last_hit;
+         search->mb_endpoint_results->data.ptrvalue = mb_results;
+      } else {
+         last_hit->next = new_hit;
+         last_hit = last_hit->next;
+      }
+   }
+   return 0;
+}
+
+Boolean WWWBlastDoSearch(WWWBlastInfoPtr theInfo)
+{
+    SeqAlignPtr  seqalign = NULL;
+    ValNodePtr  mask_loc, mask_loc_start, vnp, other_returns, error_returns;
+    TxDfDbInfoPtr dbinfo=NULL, dbinfo_head;
+    BLAST_KarlinBlkPtr ka_params=NULL, ka_params_gap=NULL;
+    BLAST_MatrixPtr matrix;
+    Int4Ptr PNTR txmatrix;
+    CharPtr params_buffer=NULL;
+    SeqAnnotPtr seqannot = NULL;
+    BlastPruneSapStructPtr prune;
+    SeqAlignPtr PNTR seqalignp = NULL;
+    Boolean is_megablast, done = FALSE, all_done = FALSE;
+    SeqLocPtr query_slp, query_lcase_mask, lcase_mask;
+    Int4 index;
+    AsnIoPtr xml_aip;
+    MegaBlastResultsPtr mb_results = NULL;
+    BLAST_OptionsBlkPtr options = theInfo->options;
+    Boolean tabular_output = (theInfo->align_view == HitTable || 
+                              theInfo->align_view == HitTableWithHeader);
+    MBXmlPtr mbxp = NULL;
+
+    if(theInfo == NULL)
+	return FALSE;
+    
+    is_megablast = options->is_megablast_search;
+
+    query_slp = theInfo->query_slp;
+    lcase_mask = query_lcase_mask = options->query_lcase_mask;
+
+    if(!theInfo->xml_output && !tabular_output && 
+       !(is_megablast && options->no_traceback)) {
+        PrintDbInformation(theInfo->database, !theInfo->db_is_na, 
+                           70, stdout, TRUE);
+    }
+
+    if(!tabular_output && options->entrez_query != NULL && 
+       theInfo->gi_list_total > 0) {
+
+        printf("Your search was limited by an Entrez query: '%s'\n"
+               "<!-- %d sequences-->\n<P>\n",
+               options->entrez_query, 
+               theInfo->gi_list_total);
+    }
+    
+    ReadDBBioseqFetchEnable ("blastall", theInfo->database, 
+                             theInfo->db_is_na, TRUE);
+    
+    if(theInfo->xml_output)
+       xml_aip = AsnIoOpen("stdout", "wx");
+    
+    while (!all_done) { /* Loop on complete BLAST searches */
+        if (!query_slp || is_megablast)
+            all_done = TRUE;
+        
+        other_returns = NULL;
+        error_returns = NULL;
+        
+        if(!theInfo->xml_output)
+            printf("</PRE>\n");
+
+        if (!is_megablast) {
+            if (SeqIdComp(SeqLocId(lcase_mask), SeqLocId(query_slp)) == 
+                SIC_YES) {
+                options->query_lcase_mask = (SeqLocPtr) ValNodeNew(NULL);
+                MemCpy(options->query_lcase_mask, lcase_mask, sizeof(SeqLoc));
+                options->query_lcase_mask->next = NULL;
+                lcase_mask = lcase_mask->next;
+            }
+            if (query_slp) {
+                seqalign = BioseqBlastEngineByLocEx(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total);
+            } else {
+                seqalign = BioseqBlastEngineEx(theInfo->fake_bsp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total);
+            }
+        } else {
+           if (options->no_traceback)
+            seqalignp = BioseqMegaBlastEngineByLoc(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total, AppendMegaBlastHit);
+           else
+            seqalignp = BioseqMegaBlastEngineByLoc(query_slp, theInfo->program, theInfo->database, options, &other_returns, &error_returns, WWWTickCallback, NULL, theInfo->gi_list, theInfo->gi_list_total, NULL);
+        }
+
+        if(!theInfo->xml_output)
+            printf("<PRE>");
+        
+        BlastErrorPrint(error_returns);
+        
+        dbinfo = NULL;
+        ka_params = NULL;
+        ka_params_gap = NULL;
+        params_buffer = NULL;
+        mask_loc = NULL;
+        matrix = NULL;
+        txmatrix = NULL;
+        for (vnp=other_returns; vnp; vnp = vnp->next) {
+            switch (vnp->choice) {
+            case TXDBINFO:
+                dbinfo = vnp->data.ptrvalue;
+                break;
+            case TXKABLK_NOGAP:
+                ka_params = vnp->data.ptrvalue;
+                break;
+            case TXKABLK_GAP:
+                ka_params_gap = vnp->data.ptrvalue;
+                break;
+            case TXPARAMETERS:
+                params_buffer = vnp->data.ptrvalue;
+                break;
+            case TXMATRIX:
+                matrix = vnp->data.ptrvalue;
+                if (matrix)
+                    txmatrix = (Int4Ptr PNTR) BlastMatrixToTxMatrix(matrix);
+                break;
+            case SEQLOC_MASKING_NOTSET:
+            case SEQLOC_MASKING_PLUS1:
+            case SEQLOC_MASKING_PLUS2:
+            case SEQLOC_MASKING_PLUS3:
+            case SEQLOC_MASKING_MINUS1:
+            case SEQLOC_MASKING_MINUS2:
+            case SEQLOC_MASKING_MINUS3:
+                if (!is_megablast)
+                    ValNodeAddPointer(&mask_loc, vnp->choice, vnp->data.ptrvalue);
+                break;
+            case BlastResponse_mbalign:
+               mb_results = (MegaBlastResultsPtr) vnp->data.ptrvalue;
+               break;
+            default:
+                break;
+            }
+        }	
+        
+        fflush(stdout);
+        
+        if (mb_results) {
+           /* Results come as alignment endpoints only from Mega BLAST */
+           MegaBlastHitPtr mb_hit = mb_results->mbhits, next_hit;
+           
+           while (mb_hit) {
+              fprintf(stdout, "%s\t%s\t%d\t%d\t%d\t%d\t%d\n", mb_hit->id1,
+                      mb_hit->id2, mb_hit->query_offset, mb_hit->subject_offset,
+                      mb_hit->query_end, mb_hit->subject_end, mb_hit->score);
+              next_hit = mb_hit->next;
+              MemFree(mb_hit->id1);
+              MemFree(mb_hit->id2);
+              MemFree(mb_hit);
+              mb_hit = next_hit;
+           }
+           MemFree(mb_results);
+           done = TRUE;
+        } else
+           done = FALSE;
+        
+        if (theInfo->xml_output && is_megablast) {
+           mbxp = PSIXmlInit(xml_aip, "megablast", theInfo->database, 
+                             options, theInfo->fake_bsp, 0);
+        }
+
+        ReadDBBioseqSetDbGeneticCode(theInfo->options->db_genetic_code);
+
+        for (index=0; !done; index++) {
+            if (is_megablast)
+                seqalign = seqalignp[index];
+            else 
+                done = TRUE;
+            if (seqalign) {
+                if(theInfo->xml_output) {
+                   if (!is_megablast) {
+                      BXMLPrintOutput(xml_aip, seqalign, options, 
+                         theInfo->program, theInfo->database, 
+                         theInfo->fake_bsp, other_returns, 0, NULL);
+                      AsnIoReset(xml_aip);
+                   } else {
+                       IterationPtr iterp;
+                       BioseqPtr bsp = BioseqLockById(SeqLocId(query_slp));
+
+                       iterp = BXMLBuildOneQueryIteration(seqalign, 
+                                  NULL, FALSE, 
+                                  !options->gapped_calculation, index, 
+                                  NULL, bsp);
+                       IterationAsnWrite(iterp, mbxp->aip, mbxp->atp);
+                       AsnIoFlush(mbxp->aip);
+                       IterationFree(iterp);
+
+                       BioseqUnlock(bsp);
+                   }
+                } else if (tabular_output) {
+                   if (theInfo->align_view == HitTableWithHeader)
+                      PrintTabularOutputHeader(theInfo->database, 
+                          theInfo->fake_bsp, query_slp, 
+                          (options->is_megablast_search ? 
+                           "megablast" : theInfo->program),
+                          0, FALSE, stdout);
+
+                   BlastPrintTabulatedResults(seqalign, theInfo->fake_bsp, 
+                        query_slp, theInfo->number_of_alignments, 
+                        theInfo->program, 
+                        !theInfo->options->gapped_calculation, FALSE, 
+                        (query_slp ? SeqLocStart(query_slp) : 0), 0, 
+                        stdout, (theInfo->align_view == HitTableWithHeader));
+                } else {
+                    seqannot = SeqAnnotNew();
+                    seqannot->type = 2;
+                    AddAlignInfoToSeqAnnot(seqannot, theInfo->align_type);
+                    seqannot->data = seqalign;
+                    
+#if !defined(NCBI_CLIENT_SERVER) && defined (NCBI_ENTREZ_CLIENT)
+                    if(theInfo->show_tax_blast) {
+                        fprintf(stdout, "<a href=#taxblast>Taxonomy reports</a><BR>");
+                    }
+#endif
+                    
+                    if (is_megablast || query_slp) {
+                        BioseqPtr bsp = BioseqLockById(SeqLocId(query_slp));
+                        init_buff_ex(85);
+                        fprintf(stdout, "<HR><BR>");
+                        AcknowledgeBlastQuery(bsp, 70, stdout, FALSE, TRUE);
+                        free_buff();
+                        BioseqUnlock(bsp);
+                    }
+                    
+                    /* Now printing nice gif with alignment overview */
+                    
+                    if(theInfo->show_overview) {
+                        Char f_name[64], title[1024], href[64];
+                        Int4 align_num;
+                        
+                        sprintf(f_name, "%ld%ld.gif", (long)random(), (long)getpid());
+                        sprintf(href, "nph-viewgif.cgi?");
+                        
+                        align_num = get_number_alignment(seqalign); 
+                        sprintf(title, 
+                                "<H3><a href=\"%s/blast/docs/newoptions.html#graphical-overview\"> "
+                                "Distribution of %ld Blast Hits on the Query Sequence</a> "
+                                "</H3>\n", 
+                                theInfo->www_root_path, (long)align_num);  
+                        
+                        
+                        /* Open HTML form */
+                        fprintf(stdout, "<FORM NAME=\"BLASTFORM\">\n");
+                        fflush(stdout);
+                        
+                        PrintAlignmentOverview(seqannot, stdout, 
+                                               "BLASTFORM", href, f_name, title); 
+                    }
+                    
+                    prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_descriptions, NULL);
+                    ObjMgrSetHold();
+                    init_buff_ex(85);
+                    PrintDefLinesFromSeqAlignEx2(prune->sap, 80, stdout, 
+                       theInfo->print_options, FIRST_PASS, NULL, -1,
+                       NULL, theInfo->www_blast_type);
+                    free_buff();
+                    
+                    prune = BlastPruneHitsFromSeqAlign(seqalign, theInfo->number_of_alignments, prune);
+                    seqannot->data = prune->sap;
+                    
+                    if(theInfo->color_schema != 0 && 
+                       (!StringICmp(theInfo->program, "blastn") || 
+                        !StringICmp(theInfo->program, "blastp"))) {
+                        
+                        if(!DDV_DisplayBlastPairList(prune->sap, mask_loc, stdout, 
+                                                     theInfo->query_is_na, 
+                                                     theInfo->align_options, 
+                                                     theInfo->color_schema)) { 
+                            fprintf(stdout, 
+                                    "\n\n!!!\n   "
+                                    "    --------  Failure to print alignment...  --------"
+                                    "\n!!!\n\n");
+                            fflush(stdout);
+                        }
+                    } else {
+
+                        if(options->is_ooframe) {
+                            printf("<PRE>");
+                            OOFShowBlastAlignment(seqalign, /*mask*/ NULL,
+                                                  stdout, theInfo->align_options, txmatrix);
+                        } else {                        
+                            if (theInfo->align_view != 0) {
+                                ShowTextAlignFromAnnot2(seqannot, 60, stdout, 
+                                   NULL, NULL, theInfo->align_options, 
+                                   txmatrix, mask_loc, NULL, NULL, 
+                                   theInfo->www_blast_type);
+                            } else {
+                                ShowTextAlignFromAnnot2(seqannot, 60, stdout, 
+                                   NULL, NULL, theInfo->align_options, 
+                                   txmatrix, mask_loc, FormatScoreFunc,
+                                   NULL, theInfo->www_blast_type);
+                            }
+                        }
+                    }
+                    seqannot->data = NULL; /* Don't want to delete seqalign yet */
+                    prune = BlastPruneSapStructDestruct(prune);
+                    ObjMgrClearHold();
+                    ObjMgrFreeCache(0);
+                }
+            } else if (!is_megablast) { /* while(seqalign) */
+                /* seqalign == NULL */
+        
+                if(theInfo->xml_output && !options->is_ooframe) {
+                    BlastErrorMsgPtr error_msg;
+                    CharPtr message;
+                    
+                    if (error_returns == NULL) {
+                        message = "No hits found";
+                    } else {
+                        error_msg = error_returns->data.ptrvalue;
+                        message = error_msg->msg;
+                    }
+                    
+                    BXMLPrintOutput(xml_aip, NULL, 
+                                    options, theInfo->program, 
+                                    theInfo->database, 
+                                    theInfo->fake_bsp, other_returns, 
+                                    0, message);
+                    
+                    if (error_returns != NULL) {
+                        MemFree(error_msg->msg);
+                        MemFree(error_msg);
+                        MemFree(error_returns);
+                    }
+                    
+                    AsnIoReset(xml_aip);
+                } else {
+                    fprintf(stdout, "\n\n ***** No hits found ******\n\n");
+                }
+            }
+            
+            if (is_megablast) { 
+                query_slp = query_slp->next;
+                if (!query_slp)
+                    done = TRUE;
+            }
+            if(!theInfo->xml_output && seqannot != NULL)
+                seqannot = SeqAnnotFree(seqannot);
+        }
+        
+        matrix = BLAST_MatrixDestruct(matrix);
+        if (txmatrix)
+            txmatrix = (Int4Ptr PNTR) TxMatrixDestruct(txmatrix);
+        
+        dbinfo_head = dbinfo;
+        if(!theInfo->xml_output && !tabular_output && 
+           !(is_megablast && options->no_traceback)) {        
+            fprintf(stdout, "<PRE>");
+            init_buff_ex(85);
+            while (dbinfo) {
+                PrintDbReport(dbinfo, 70, stdout);
+                dbinfo = dbinfo->next;
+            }
+        }
+        
+        dbinfo_head = TxDfDbInfoDestruct(dbinfo_head);
+        
+        if (ka_params) {
+            if(!theInfo->xml_output && !tabular_output && 
+               !(is_megablast && options->no_traceback)) {        
+                PrintKAParameters(ka_params->Lambda, ka_params->K, 
+                                  ka_params->H, 70, stdout, FALSE);
+            }
+            MemFree(ka_params);
+        }
+        
+        if (ka_params_gap) {
+            if(!theInfo->xml_output && !tabular_output &&
+               !(is_megablast && options->no_traceback)) {        
+                PrintKAParameters(ka_params_gap->Lambda, ka_params_gap->K,
+                                  ka_params_gap->H, 70, stdout, TRUE);
+            }
+            MemFree(ka_params_gap);
+        }
+        
+        if(!theInfo->xml_output && !tabular_output && 
+           !(is_megablast && options->no_traceback)) {        
+            
+            PrintTildeSepLines(params_buffer, 70, stdout);
+            
+#if !defined(NCBI_CLIENT_SERVER) && defined (NCBI_ENTREZ_CLIENT)
+            
+            fprintf(stdout, "<HR>\n");
+            
+            if( !tabular_output && theInfo->show_tax_blast) {
+                TXBHtmlReport(seqalign, stdout, theInfo->query_is_na,
+                              theInfo->db_is_na, theInfo->database, 
+                              NULL, NULL, theInfo->show_gi);
+            }
+            
+#endif
+        }
+        
+        if (is_megablast) {
+            Int4 i;
+            for (i=0; i<index; i++)
+                SeqAlignSetFree(seqalignp[i]);
+            MemFree(seqalignp);
+        } else if(seqalign != NULL)
+            seqalign = SeqAlignSetFree(seqalign);
+        
+        MemFree(params_buffer);
+        free_buff();
+        
+        mask_loc_start = mask_loc;
+        while (mask_loc) {
+            SeqLocSetFree(mask_loc->data.ptrvalue);
+            mask_loc = mask_loc->next;
+        }
+        ValNodeFree(mask_loc_start);
+        
+        other_returns = ValNodeFree(other_returns);
+        
+        if (!is_megablast && query_slp) {
+            query_slp = query_slp->next;
+            if (!query_slp)
+                all_done = TRUE;
+        }
+    } /* End of loop over all searches */
+
+    SeqLocSetFree(query_lcase_mask);
+
+    if (theInfo->xml_output) {
+       if (is_megablast && mbxp != NULL)
+          MBXmlClose(mbxp, other_returns, !options->gapped_calculation);
+    }
+    ReadDBBioseqFetchDisable();
+
+    if (!theInfo->xml_output)
+       fprintf(stdout, "</PRE>\n</BODY>\n</HTML>\n");
+
+    return TRUE;
+}
+
+static void WWWBlastPrintTopHeader(WWWBlastInfoPtr theInfo)
+{
+    fprintf(stdout, "<HTML>\n");
+    fprintf(stdout, "<TITLE>BLAST Search Results</TITLE>\n"); 
+    fflush(stdout);
+    
+    fprintf(stdout, "<BODY BGCOLOR=\"#FFFFFF\" LINK=\"#0000FF\" "
+            "VLINK=\"#660099\" ALINK=\"#660099\">\n");
+    fprintf(stdout, "<map name=img_map1>\n");
+    fprintf(stdout, "<area shape=rect coords=2,1,48,21 "
+            "href=\"http://www.ncbi.nlm.nih.gov\">\n");
+    fprintf(stdout, "<area shape=rect coords=385,1,435,21 "
+            "href=\"%s/blast/index.html\">\n", theInfo->www_root_path);
+    fprintf(stdout, "<area shape=rect coords=436,1,486,21 "
+            "href=\"http://www.ncbi.nlm.nih.gov/Entrez/\">\n");
+    fprintf(stdout, "<area shape=rect coords=487,1,508,21 "
+            "href=\"%s/blast/docs/blast_help.html\">\n", theInfo->www_root_path);
+    fprintf(stdout, "</map>\n"); 
+    fprintf(stdout, "<IMG USEMAP=#img_map1 WIDTH=509 HEIGHT=22 "
+            "SRC=\"%s/blast/images/blast_results.gif\" ISMAP> \n", 
+            theInfo->www_root_path);
+}
+
+void WWWBlastPrintHeader(WWWBlastInfoPtr theInfo)
+{
+
+    fprintf(stdout, "<PRE>\n");
+    init_buff_ex(90);
+    if (theInfo->options->is_megablast_search) {
+        BlastPrintVersionInfo("megablast", TRUE, stdout);
+    } else if (theInfo->options->is_rps_blast){
+        BlastPrintVersionInfo("rps-blast", TRUE, stdout);
+    } else if (theInfo->options->is_ooframe){
+        BlastPrintVersionInfo("OOF BLASTX", TRUE, stdout);
+    } else {
+        BlastPrintVersionInfo(theInfo->program, TRUE, stdout);
+        fprintf(stdout, "\n");
+        BlastPrintReference(TRUE, 90, stdout);
+    }
+    fprintf(stdout, "\n");
+    if (!theInfo->options->is_megablast_search && !theInfo->query_slp)
+       AcknowledgeBlastQuery(theInfo->query_bsp, 70, stdout, 
+                             theInfo->believe_query, TRUE);
+    free_buff();
+
+    return;
+}
+
+Int2 Main(void)
+{
+    WWWBlastInfoPtr theInfo;
+
+    UseLocalAsnloadDataAndErrMsg ();
+            
+    if (! SeqEntryLoad())
+        return 1;
+    
+    ErrSetMessageLevel(SEV_WARNING);
+
+    /* This function will read posting data, set-up config file and
+       write small message into logfile (if it exists) */
+    
+    if((theInfo = WWWBlastReadArgs(NULL)) == NULL)
+        return 1;
+    
+    if (!theInfo->xml_output) 
+       WWWBlastPrintTopHeader(theInfo);
+
+    /* Read options into structure */
+    if(!WWWCreateSearchOptions(theInfo)) {
+        return 1;
+    }
+    
+    /* validate them */
+    if(!WWWValidateOptions(theInfo)) {
+        return 1;
+    }
+
+    /* Print BLAST Header */
+
+    if(!theInfo->xml_output && 
+       theInfo->align_view != HitTableWithHeader) {        
+        WWWBlastPrintHeader(theInfo);
+    }
+
+    /* Do the search and Format output */
+
+#ifdef NCBI_CLIENT_SERVER
+    WWWBlastDoClientSearch(theInfo);
+#else
+    WWWBlastDoSearch(theInfo);
+#endif
+
+    WWWBlastInfoFree(theInfo);
+
+    return 0;
+}
diff --git a/network/wwwblast/Src/wwwblast.h b/network/wwwblast/Src/wwwblast.h
new file mode 100644
index 00000000..7df7f90c
--- /dev/null
+++ b/network/wwwblast/Src/wwwblast.h
@@ -0,0 +1,243 @@
+/* $Id: wwwblast.h,v 1.2 2003/05/13 22:00:37 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: wwwblast.h,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Creation Date: 03/15/2000
+*
+* $Revision: 1.2 $
+*
+* File Description:
+*        Definitions for standalone WWW Blast CGI program.
+*
+* $Log: wwwblast.h,v $
+* Revision 1.2  2003/05/13 22:00:37  dondosha
+* More changes to make alternative links work
+*
+* Revision 1.1  2002/12/02 18:05:54  dondosha
+* Moved from different locations to a common one
+*
+* Revision 6.10  2002/04/19 17:47:24  dondosha
+* Removed restriction on the allowed number of databases in the config file
+*
+* Revision 6.9  2002/01/08 22:36:25  dondosha
+* Added tabular output functionality
+*
+* Revision 6.8  2000/10/31 20:17:13  shavirin
+* Added definition of the function TestSTDOut(void);
+*
+* Revision 6.7  2000/09/27 22:18:04  shavirin
+* Added possibility to limit search to results of entrez query.
+*
+* Revision 6.6  2000/09/12 22:00:24  dondosha
+* Added matrix to BLASTPrintData structure
+*
+* Revision 6.5  2000/09/08 20:15:12  dondosha
+* Added WWWBlastErrMessageEx, taking a CharPtr seq_info argument
+*
+* Revision 6.4  2000/09/05 15:25:20  shavirin
+* Added #include <mblast.h> to remove warning.
+*
+* Revision 6.3  2000/08/28 20:20:21  dondosha
+* Added a SeqLoc linked list argument to WWWBlastInfo structure for multiple query search
+*
+* Revision 6.2  2000/08/09 20:29:16  shavirin
+* Added new parameters to the info structure xml_output and CHARPosFreqs
+*
+* Revision 6.1  2000/05/17 15:52:42  shavirin
+* Initial revision in new location.
+*
+*
+* ==========================================================================
+*/
+
+#include <ncbi.h>
+#include <blastdef.h>
+#include <blast.h>
+#include <blastpri.h>
+#include <sequtil.h>
+#include <txalign.h>
+#include <salogif.h>
+#include <ddvcreate.h>
+#include <objblst3.h>
+#include <mblast.h>
+
+#ifdef NCBI_CLIENT_SERVER
+#include <netblap3.h>
+#endif
+
+typedef enum {
+    BLASTNoError         =   0,   /* no error             */
+    BLASTNetwork         =  -1,
+    BLASTNoSpace         =  -2,
+    BLASTBadFileName     =  -3,
+    BLASTNotImplemented  =  -4,
+    BLASTErrProgram      =  -5,  /* program missing from posting data    */
+    BLASTErrDatalib      =  -6,  /* datalib missing from posting data    */
+    BLASTErrProgName     =  -7,  /* program name is not supported        */
+    BLASTErrNoSequence   =  -8,  /* NULL sequence passed to the engine   */
+    BLASTErrCombination  =  -9,  /* Invalid program/database combination */
+    BLASTNoMemory        =  -10, /* too bad ...                          */
+    BLASTNCBI_DATA       =  -11, /* DATA files missing on any path       */
+    BLASTFastaToSE       =  -12, /* FastaToSeqEntry() returned NULL      */
+    BLASTErrOptions      =  -13, /* Badly formatted options              */
+    BLASTErrNoQueue      =  -14, /* Queue overloaded */
+    BLASTConfigFile      =  -15, /* Error reading config file */
+    BLASTEntrez          =  -16, /* Cannot connect to Entrez */  
+    BLASTAccesssion      =  -17, /* Invalid of unavailable accession */  
+    BLASTSendmail        =  -18, /* Cannot start sendmail process */ 
+    BLASTAddress         =  -19, /* Invalid return address */
+    BLASTOptionStr       =  -20, /* Invalidly formatted advanced string */
+    BLASTErrAccType      =  -21, /* wrong type of sequence identifier */
+    BLASTErrClient       =  -22, /* cannot connect to the Blast service */
+    BLASTErrServer       =  -23, /* Error from the server side */
+    BLASTMiscError       =  -99  /* undefined internal error             */
+} BLASTErrCode;
+
+#define INIT_DB_NUM 256
+
+/* Max. total number of concurrent running requests */
+#define DEFAULT_RUN_MAX            2 
+
+/* Max. total number of waiting requests */
+#define DEFAULT_QUEUE_MAX          100 
+#define NUM_CPU_TO_USE             4
+#define DEFAULT_DESCRIPTIONS    100
+#define DEFAULT_ALIGNMENTS       50 
+#define DEFAULT_EXPECT           10
+
+/* CPU time limit. */
+#define DEFAULT_CPU_LIMIT 3600
+
+typedef struct BLASTConfig {
+    Int4 run_max;
+    Int4 queue_max;
+    Int4 num_cpu;
+    Int4 niceval;
+    Int2 num_dbs;
+    Int2 db_num_allocated;
+    CharPtr PNTR allow_db;
+} BLASTConfig, PNTR BLASTConfigPtr;
+
+typedef enum {
+ Pairwise = 0,
+ QueryAnchoredIdent = 1,
+ QueryAnchoredNoIdent = 2,
+ FlatQueryAnchoredIdent = 3,
+ FlatQueryAnchoredNoIdent = 4,
+ QueryAnchoredBluntEnd = 5,
+ FlatQueryAnchoredBluntEnd = 6,
+ BlastXML = 7,
+ HitTable = 8,
+ HitTableWithHeader = 9
+} BLASTAlignView;
+
+typedef struct _www_blast_info {
+    BLAST_OptionsBlkPtr options;
+    WWWInfoPtr info;
+    BLASTErrCode error_code;
+    CharPtr ConfigFile;
+    CharPtr program, database, blast_type;
+    BioseqPtr query_bsp;
+    BioseqPtr fake_bsp;
+    Int4 number_of_descriptions, number_of_alignments;
+    Boolean query_is_na, db_is_na, align_type, show_gi, show_overview;
+    Boolean believe_query;
+    Uint4 align_options, print_options;
+    BLASTAlignView align_view;
+    Int4 input_type, color_schema;
+    Boolean is_phi_blast;
+    Boolean show_tax_blast;
+    Boolean xml_output;
+    BLASTConfigPtr blast_config;
+    CharPtr www_root_path;
+    SeqLocPtr query_slp; /* For multiple query search */
+    /* Limitation to list of gis - due to may be entrez query */
+    BlastDoubleInt4Ptr gi_list;
+    Int4 gi_list_total;
+    CharPtr www_blast_type;
+} WWWBlastInfo, PNTR WWWBlastInfoPtr;
+
+
+/* Structures used in PHI/PSI Blast searches */
+
+typedef struct GIList {
+    Int4  gi;
+    struct GIList  *next;
+} GIList, PNTR GIListPtr;
+
+typedef struct PSIData {
+    CharPtr  matrix62;
+    CharPtr  CHARPosFreqs;
+    GIListPtr	PrevCheckedGIs;
+    GIListPtr	PrevGoodGIs;
+    Int4 StepNumber;
+    Nlm_FloatHi karlinK;
+} PSIData, PNTR PSIDataPtr;
+
+typedef struct BLASTPrintData {
+    SeqAlignPtr        seqalign;
+    BLAST_KarlinBlkPtr ka_params, ka_params_gap;
+    TxDfDbInfoPtr      dbinfo;
+    CharPtr            buffer;  
+    ValNodePtr         mask_loc;	  
+    PSIDataPtr         psidata;
+    SeqLocPtr          seqloc;
+    ValNodePtr	       vnp;	/* PHI-BLAST output. */
+    ValNodePtr         info_vnp; /* PHI-Blast info strings */
+    BLAST_MatrixPtr    matrix; /* Needed for the positives computation */
+} BLASTPrintData, PNTR BLASTPrintDataPtr;
+
+
+/* ------------------------------------------- */
+void WWWBlastInfoFree(WWWBlastInfoPtr theInfo);
+
+void WWWBlastErrMessageEx(BLASTErrCode error_code, CharPtr error_msg, 
+                          CharPtr seq_info);
+
+void WWWBlastErrMessage(BLASTErrCode error_code, CharPtr error_msg);
+
+WWWBlastInfoPtr WWWBlastReadArgs(CharPtr type);
+
+Boolean BLAST_Time(CharPtr string, Int4 len, time_t seconds);
+
+Boolean WWWValidateOptions(WWWBlastInfoPtr theInfo);
+
+Boolean WWWCreateSearchOptions(WWWBlastInfoPtr theInfo);
+
+Boolean TestSTDOut(void);
+
+/* PSI/PHI Blast-related function */
+
+void BLASTPrintDataFree(BLASTPrintDataPtr data);
+
+Boolean SplitSeqAlign(SeqAlignPtr seqalign, SeqAlignPtr *GoodSeqAlignment_ptr, SeqAlignPtr *BadSeqAlignment_ptr, SeqAlignPtr *lastGood_ptr, Int2Ptr *marks_ptr, Int2Ptr countBad_ptr, Int2Ptr countGood_ptr, Nlm_FloatHi ethresh_old);
+
+BLASTPrintDataPtr PSIBlastSearch(WWWBlastInfoPtr theInfo);
+
+BLASTPrintDataPtr PHIBlastSearch(WWWBlastInfoPtr theInfo);
+
diff --git a/network/wwwblast/Src/wwwbutl.c b/network/wwwblast/Src/wwwbutl.c
new file mode 100644
index 00000000..9f734288
--- /dev/null
+++ b/network/wwwblast/Src/wwwbutl.c
@@ -0,0 +1,3103 @@
+/* $Id: wwwbutl.c,v 1.18 2003/08/13 14:35:33 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: wwwbutl.c,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 04/21/2000
+*
+* $Revision: 1.18 $
+*
+* File Description:
+*         WWW BLAST/PSI/PHI utilities
+*
+* $Log: wwwbutl.c,v $
+* Revision 1.18  2003/08/13 14:35:33  dondosha
+* When no percent identity cutoff, default value for mismatch penalty is -3 for blastn
+*
+* Revision 1.17  2003/07/15 15:07:39  dondosha
+* Added NO_REFERENCE URL option to skip printing citation in BLAST report
+*
+* Revision 1.16  2003/06/16 19:19:29  dondosha
+* Fixed memory allocation for lines and words when reading config file
+*
+* Revision 1.15  2003/05/21 18:49:25  dondosha
+* Bug fix in setting subsequence range
+*
+* Revision 1.14  2003/05/13 22:00:37  dondosha
+* More changes to make alternative links work
+*
+* Revision 1.13  2003/05/13 21:17:01  dondosha
+* Pass www_blast_type to txalign in all cases
+*
+* Revision 1.12  2003/05/09 21:09:05  dondosha
+* Removed unused variables
+*
+* Revision 1.11  2003/05/09 17:50:41  dondosha
+* Fixed bug for database genetic code option
+*
+* Revision 1.10  2003/05/05 18:14:38  dondosha
+* Added subsequence options
+*
+* Revision 1.9  2003/05/02 23:04:03  dondosha
+* Fixed paths for non-standard setups, removed blast_form.map
+*
+* Revision 1.8  2003/04/29 15:55:56  dondosha
+* Always use root path in links
+*
+* Revision 1.7  2003/04/04 22:40:44  dondosha
+* Removed limit for the length of a line in the config file
+*
+* Revision 1.6  2003/03/03 21:44:26  dondosha
+* Removed "/blast" from path to nph-viewgif.cgi in PSI/PHI output
+*
+* Revision 1.5  2003/02/10 21:48:36  dondosha
+* Correction for multiple queries in form of accession
+*
+* Revision 1.4  2003/01/10 21:50:22  bealer
+* - Modify to return errors from BLASTGetUidsFromQuery instead of logging them.
+*
+* Revision 1.3  2003/01/03 22:11:23  dondosha
+* Allow multiple lines with database lists for the same program
+*
+* Revision 1.2  2002/12/02 21:21:22  dondosha
+* 1. Use centralized utility to parse other advanced options;
+* 2. Made it possible to use URL variable names same as in the NCBI BLAST URL API.
+*
+* Revision 1.1  2002/12/02 18:05:53  dondosha
+* Moved from different locations to a common one
+*
+* Revision 6.33  2002/08/06 20:10:10  dondosha
+* Added handling of the discontiguous word options
+*
+* Revision 6.32  2002/05/09 15:38:08  dondosha
+* Call BLASTOptionNewEx instead of BLASTOptionNew, so megablast defaults are set in a central place
+*
+* Revision 6.31  2002/05/02 22:45:47  dondosha
+* Do not break out of loop if SeqPortRead returns negative value, just skip the non-residue and continue
+*
+* Revision 6.30  2002/04/19 17:47:24  dondosha
+* Removed restriction on the allowed number of databases in the config file
+*
+* Revision 6.29  2002/03/19 23:30:19  dondosha
+* Do not increment options->wordsize by 4 for megablast any more
+*
+* Revision 6.28  2002/01/08 22:36:24  dondosha
+* Added tabular output functionality
+*
+* Revision 6.27  2001/09/06 20:24:34  dondosha
+* Removed threshold_first
+*
+* Revision 6.26  2001/07/20 19:56:04  dondosha
+* Scale cutoff_s2 for megablast if match reward not 1
+*
+* Revision 6.25  2001/02/16 15:53:17  dondosha
+* Cosmetic change
+*
+* Revision 6.24  2001/01/05 18:18:28  dondosha
+* Change reward and penalty scores depending on percent identity
+*
+* Revision 6.23  2001/01/05 18:07:15  dondosha
+* Added handling of word size and percent identity fields for options creation
+*
+* Revision 6.22  2000/11/16 22:35:40  dondosha
+* Added lower case masking option and endpoints results option
+*
+* Revision 6.21  2000/10/31 20:21:26  shavirin
+* Fixed bug with RedoAlignmentCore filtering.
+*
+* Revision 6.20  2000/10/16 22:18:35  shavirin
+* Added possibility to perform OOF blastx
+*
+* Revision 6.19  2000/10/16 20:26:35  shavirin
+* Added possibility to rum RPS Blast.
+*
+* Revision 6.18  2000/09/28 16:32:53  dondosha
+* Compiler warning fix
+*
+* Revision 6.17  2000/09/27 22:18:03  shavirin
+* Added possibility to limit search to results of entrez query.
+*
+* Revision 6.16  2000/09/12 22:01:42  dondosha
+* Use matrix returned from search during formatting
+*
+* Revision 6.15  2000/09/08 20:16:59  dondosha
+* Print informative error messages for bad accessions, still do search if at least one accession is good
+*
+* Revision 6.14  2000/09/08 17:46:54  dondosha
+* Allow multiple accessions in input
+*
+* Revision 6.13  2000/09/07 18:02:58  dondosha
+* If query has many sequences, put them in a SeqLoc list
+*
+* Revision 6.12  2000/09/01 21:47:34  dondosha
+* Make check for wordsize too small; add 4 to user-supplied wordsize for megablast
+*
+* Revision 6.11  2000/09/01 17:50:59  dondosha
+* No part of SeqEntry can be freed before the very end
+*
+* Revision 6.10  2000/09/01 17:30:26  dondosha
+* Small corrections for megablast with Entrez client
+*
+* Revision 6.9  2000/08/30 22:20:24  dondosha
+* Small changes for megablast web page
+*
+* Revision 6.8  2000/08/28 20:17:42  dondosha
+* Added functionality for megablast web page
+*
+* Revision 6.7  2000/08/10 18:17:19  shavirin
+* Used correct (fake) Bioseq in printing alignmenets.
+*
+* Revision 6.6  2000/08/10 14:50:37  shavirin
+* Fixed 64 dependent bug
+*
+* Revision 6.4  2000/08/09 20:49:01  shavirin
+* Added support for S&W Blast and XML output.
+*
+* Revision 6.3  2000/07/31 20:39:23  shavirin
+* Some formating changes from Haruna Cofer (haruna@detroit.sgi.com)
+*
+* Revision 6.2  2000/07/26 02:26:16  shavirin
+* Changes in accordance to Alejandro's S&W Blast.
+*
+* Revision 6.1  2000/05/17 15:53:40  shavirin
+* Initial revision.
+*
+*
+* ==========================================================================
+*/
+
+#include <wwwblast.h>
+
+void WWWBlastInfoFree(WWWBlastInfoPtr theInfo)
+{
+    Int4 i;
+    WWWInfoFree(theInfo->info);
+    BLASTOptionDelete(theInfo->options);
+    MemFree(theInfo->database);
+    MemFree(theInfo->program);
+
+    for(i = 0; i < theInfo->blast_config->num_dbs; i++) {
+        MemFree(theInfo->blast_config->allow_db[i]);
+    }
+    MemFree(theInfo->blast_config->allow_db);
+    MemFree(theInfo->blast_config);
+
+    /* if(!theInfo->believe_query)
+       fake_bsp = BlastDeleteFakeBioseq(fake_bsp); */
+
+    MemFree(theInfo->blast_type);
+    MemFree(theInfo->www_blast_type);
+    MemFree(theInfo->ConfigFile);
+    SeqLocSetFree(theInfo->query_slp);
+    MemFree(theInfo->www_root_path);
+    MemFree(theInfo);
+
+    return;
+}
+
+void WWWBlastErrMessage(BLASTErrCode error_code, CharPtr error_msg)
+{
+   WWWBlastErrMessageEx(error_code, error_msg, NULL);
+}
+
+void WWWBlastErrMessageEx(BLASTErrCode error_code, CharPtr error_msg,
+                          CharPtr seq_info)
+{
+    CharPtr delim = "<BR>";
+
+    if(error_code == BLASTNoError)
+	return;
+
+    fprintf(stdout, "<FONT color=red><h3>");
+    fprintf(stdout, "Error %ld in submitting BLAST query", labs(error_code));
+    if (seq_info)
+       fprintf(stdout, "</h3></FONT> <BR> <b> Accession: %s </b> <BR> <HR>\n<b>", seq_info);
+    else
+       fprintf(stdout, "</h3></FONT><HR>\n<b>");
+    fprintf(stdout, "Short error description:");
+    
+    fprintf(stdout, "</b><BR><BR>\n");
+    switch(error_code) {
+        
+    case BLASTEntrez:
+        
+        fprintf(stdout,
+                "Your input sequence may not be found in Entrez %s"
+                "or Entrez access interface currently unavailable. %s"
+                "Please send message to blast_help@ncbi.nlm.nih.gov %s"
+                "with description of your query", 
+                delim, delim, delim);
+        break;
+        
+    case BLASTFastaToSE:
+        
+        fprintf(stdout,
+                "Your input sequence formatted incorrectly. %s"
+                "Please read blast help if you have problems with formatting %s"
+                "or send request to blast help account.", 
+                delim, delim);
+        break;
+        
+    case BLASTErrNoSequence:
+        
+        fprintf(stdout,
+                "Input sequence for the BLAST search, probably missing. %s"
+                "Please see the blast help for a description %s"
+                "of the FASTA sequence format.", 
+                delim, delim);
+        break;
+        
+    case BLASTErrCombination:
+        
+        fprintf(stdout, 
+                "The combination of database and program, that you provided in your %s"
+                "message is invalid or not acceptable by BLAST search system. %s"
+                "Please look at current possible combinations in BLAST help. ",
+                delim, delim);
+        break;
+        
+    case BLASTErrAccType:
+        
+        fprintf(stdout, 
+                "You specified a protein (or nucleotide) sequence identifier, %s"
+                "but a nucleotide (or protein) sequence is required for your search.",
+                delim);
+        
+        break;
+        
+    case BLASTErrDatalib:
+        
+        fprintf(stdout, "No database was specified.  ");
+        break;
+        
+    case BLASTErrNoQueue:
+        fprintf(stdout, 
+                "Unable to accept more BLAST jobs right now, %s"
+                "Queue overloaded. Please try again later.", 
+                delim);
+        break;
+
+    case BLASTOptionStr:
+        
+        if(error_msg != NULL) {
+            fprintf(stdout, "%s", error_msg);
+        }
+        break;
+        
+    case BLASTMiscError:
+    default:
+        
+        if(error_msg != NULL) {
+            fprintf(stdout, "%s %s", error_msg, delim);
+        } else {
+            fprintf(stdout, 
+                    "There were some internal software problems while processing %s"
+                    "your request. Please contact blast support with a full %s"
+                    "description of your query to BLAST as soon as possible.",
+                    delim, delim); 
+        }
+        break;
+    }
+    
+    fprintf(stdout, "\n<HR>\n");
+
+    printf("</BODY>\n");
+    printf("</HTML>\n");
+    fflush(stdout);
+    return;
+}
+
+Boolean BLAST_Time(CharPtr string, Int4 len, time_t seconds)
+{
+    CharPtr chptr;
+    
+    if(string == NULL || len < 25)
+	return FALSE;
+    
+    if(!seconds) {
+	seconds = GetSecs();
+    }
+    
+    if((chptr = ctime(&seconds)) != NULL) 
+        StringCpy(string, chptr);
+    
+    string[24] = NULLB;
+    return TRUE;
+}
+
+WWWBlastInfoPtr WWWBlastReadArgs(CharPtr type)
+{
+    WWWBlastInfoPtr theInfo;
+    CharPtr blast_type, hostname, chptr;
+    Char tmp[256];
+    FILE *log_fd;
+
+    theInfo = MemNew(sizeof(WWWBlastInfo));
+    
+    if(WWWGetArgs(&theInfo->info) != WWWErrOk) {
+        WWWBlastErrMessage(BLASTMiscError, NULL);
+        return NULL;    
+    }
+
+    if((chptr = WWWGetQuery(theInfo->info)) == NULL || *chptr == NULLB) {
+        fprintf(stdout, "<META HTTP-EQUIV=\"Refresh\" "
+                "CONTENT=\"2; URL=%s.html\">", type ? type : "blast");
+        return NULL;
+    }
+    
+#ifdef PRINT_ALL_INPUT  /* Printing out all coming data for debugging */
+  {
+    Int4 index;
+    for(index= 0; index < WWWGetNumEntries(theInfo->info); index ++) {
+        printf("%s : %s<BR>", 
+               WWWGetNameByIndex(theInfo->info, index), 
+               WWWGetValueByIndex(theInfo->info, index));
+    }
+  }
+#endif
+    
+    if(getenv("DEBUG_COMMAND_LINE") != NULL) {
+        FILE *fd;
+        fd = FileOpen("/tmp/__web.in", "w");
+        fprintf(fd, "%s", ((WWWInfoDataPtr)theInfo->info)->query);
+        FileClose(fd);
+    }
+
+    /* Root path for PSI/PHI Blast images */ 
+    if ((chptr = getenv("WWW_ROOT_PATH")) != NULL)
+       theInfo->www_root_path = StringSave(chptr);
+    else
+       theInfo->www_root_path = StringSave("..");
+
+    if ( !ErrSetLogfile ("/dev/null", ELOG_APPEND) ) {
+        fprintf(stdout, "Cannot set logfile exiting....\n");
+        return FALSE;
+    } else {
+        ErrSetOpts (ERR_CONTINUE, ERR_LOG_ON);
+    }
+    
+    /* Config file with program/database relationsship */
+    
+    blast_type = WWWGetValueByName(theInfo->info, "BLAST_TYPE");
+    
+    if(blast_type == NULL || *blast_type == NULLB) {
+        theInfo->blast_type = StringSave(type ? type : "blast");
+        sprintf(tmp, "%s.rc", theInfo->blast_type); 
+        theInfo->ConfigFile = StringSave(tmp);
+    } else {
+        sprintf(tmp, "%s.rc", blast_type);
+        theInfo->blast_type = StringSave(blast_type);
+        theInfo->ConfigFile = StringSave(tmp);
+    }
+    
+    sprintf(tmp, "%s.log", blast_type == NULL? "wwwblast" : blast_type);
+
+    /* The following is used for links in formatted output */
+    theInfo->www_blast_type = WWWGetValueByName(theInfo->info, "WWW_BLAST_TYPE");
+
+    log_fd = FileOpen(tmp, "a"); 
+
+    if(log_fd == NULL) /* If log_fd == NULL - no problem */
+        return theInfo;
+    
+    BLAST_Time(tmp, sizeof(tmp), 0);
+
+    if((hostname = getenv("PROXIED_IP")) == NULL)
+        hostname = WWWGetAddress(theInfo->info);
+    
+    fprintf(log_fd, "\n%d|%s|%s|%s",
+            getpid(), tmp, hostname == NULL? "host_not_set" : hostname,
+            WWWGetAgent(theInfo->info));
+    
+    FileClose(log_fd);
+    
+    return theInfo;
+}
+
+/* Set of functions to handle BLAST custom configuration file */
+static BLASTConfigPtr BLASTConfigNew(void)
+{
+    BLASTConfigPtr config;
+    
+    if((config = (BLASTConfigPtr) MemNew(sizeof(BLASTConfig))) == NULL)
+	return NULL;
+    
+    config->run_max = DEFAULT_RUN_MAX;
+    config->queue_max = DEFAULT_QUEUE_MAX;
+    config->num_cpu = NUM_CPU_TO_USE;
+    config->allow_db = (CharPtr PNTR) MemNew(INIT_DB_NUM*sizeof(CharPtr));
+    config->db_num_allocated = INIT_DB_NUM;
+
+    return config;
+}
+static Int4 BLASTEatWs (FILE* fp)
+{
+    Int4 ch;
+
+    while ((ch = fgetc (fp)) != EOF) {
+	if (ch != ' ' && ch != '\t')
+	    return ch;
+    }
+    return ch;
+}
+
+static void BLASTConfigGetWord(CharPtr word, CharPtr PNTR line_ptr) 
+{
+    Int4 x = 0, y = 0;
+    CharPtr line = *line_ptr;
+    
+    for(x=0; line[x] && IS_WHITESP(line[x]); x++);
+
+    while(TRUE) {
+       if(!(word[y] = line[x]))
+          break;
+       if(IS_WHITESP(line[x]))
+          if((!x) || (line[x-1] != '\\'))
+             break;
+       if(line[x] != '\\') ++y;
+       ++x;
+    }
+    word[y] = '\0';
+    
+    while(line[x] && IS_WHITESP(line[x])) ++x;
+
+    *line_ptr = &line[x];
+}
+
+static Int4 BLASTConfigGetLine (CharPtr PNTR line, Int4Ptr size, FILE* fp)
+{
+    int   len = 0, ch;
+    CharPtr s = *line, new_s;
+    Int4 n = *size;
+
+    ch = BLASTEatWs(fp);
+
+    while (TRUE) {
+       if (ch == EOF || ch == '\n') {
+          if (len && s[len - 1] == ' ') s[len - 1] = '\0';
+          else s[len] = '\0';
+          break;
+       } else if (len >= n-2) {
+          if ((new_s = Realloc(s, 2*n)) == NULL) {
+             if (len && s[len - 1] == ' ') s[len - 1] = '\0';
+             else s[len] = '\0';
+             break;
+          }
+          n *= 2;
+          s = new_s;
+       }
+       s[len++] = ch;
+       ch = fgetc (fp);
+       
+       if (ch == '\t' || ch == ' ') {
+          s[len++] = ch;
+          ch = BLASTEatWs(fp);
+       }
+    }
+    *line = s;
+    *size = n;
+
+    return feof(fp) ? 1 : 0;
+}
+
+#define MAX_LINE_SIZE 2048
+static BLASTConfigPtr BLASTReadConfigFile(CharPtr filename, CharPtr program)
+{
+    FILE *fd;
+    BLASTConfigPtr config;
+    CharPtr line, word, line_start;
+    Int4 value, i;
+    Int4 line_size = MAX_LINE_SIZE;
+    
+    if(filename == NULL)
+	return NULL;
+    
+    if((config = BLASTConfigNew()) == NULL)
+       return NULL;
+    
+    if((fd = FileOpen(filename, "r")) == NULL)
+       return NULL;
+
+    line_start = line = Malloc(line_size);
+    word = Malloc(line_size);
+
+    while(!(BLASTConfigGetLine(&line_start, &line_size, fd))) {
+       line = line_start;
+       if((line[0] != '#') && (line[0] != '\0')) {
+          BLASTConfigGetWord(word, &line);
+          
+          if(!StringICmp(word, "RunMaxProcesses") && 
+             (value = atoi(line)) != 0) {
+             config->run_max = value;
+          } else if(!StringICmp(word, "QueueMaxJobs") && 
+                    (value = atoi(line)) != 0) {
+             config->queue_max = value;
+          } else if(!StringICmp(word, "NumCpuToUse") && 
+                    (value = atoi(line)) != 0) {
+             config->num_cpu = value;
+          } else if(!StringICmp(word, "NiceValue") && 
+                    (value = atoi(line)) != 0) {
+             config->niceval = value;
+          } else if(!StringICmp(word, program)) {
+             for(i = config->num_dbs; line[0] != NULLB; i++) {
+                BLASTConfigGetWord(word, &line);
+                if (i >= config->db_num_allocated) {
+                   CharPtr PNTR ptr;
+                   if ((ptr = (CharPtr PNTR)
+                        Realloc(config->allow_db, 
+                                2*config->db_num_allocated*sizeof(CharPtr)))
+                       != NULL) {
+                      config->allow_db = ptr;
+                      config->db_num_allocated *= 2;
+                   } else {
+                      break;
+                   }
+                }
+                config->allow_db[i] = StringSave(word);
+             }
+             config->num_dbs = i;
+          }
+       }
+    }
+
+    MemFree(line_start);
+    MemFree(word);
+
+    FileClose(fd);
+    return config;
+}
+
+static Boolean ValidateCombinationsEx(WWWBlastInfoPtr theInfo, 
+                                      CharPtr database)
+{
+    Int4 i;
+    
+    for(i = 0; i < theInfo->blast_config->num_dbs; i++) {
+	if(!StringICmp(database, theInfo->blast_config->allow_db[i]))
+	    return TRUE;
+    }
+    return FALSE;
+}
+
+/* This will work if search require to choose few databases */
+static Boolean WWWParseDatabases(WWWBlastInfoPtr theInfo)
+{
+    Int4  count, index;
+    Boolean done, datalib_found;
+    Char buffer[4096], buffer1[4096]; /* is 4096 always long enough? XXX */
+    CharPtr ptr, chptr;
+
+    count = WWWGetNumEntries(theInfo->info);
+    datalib_found = FALSE;
+    ptr = buffer;
+    
+    for (index=0; index<count; index++) {
+	chptr = WWWGetNameByIndex(theInfo->info, index);
+	if (StringCmp(chptr, "DATALIB") == 0 || 
+            StringCmp(chptr, "DATABASE") == 0) {
+	    datalib_found = TRUE;
+	    chptr = WWWGetValueByIndex(theInfo->info, index);
+	    done = FALSE;
+            
+            /* Parse string if multiple database names. */
+	    while (done == FALSE) { 
+		done = readdb_parse_db_names(&chptr, buffer1);
+		if (ValidateCombinationsEx(theInfo, buffer1) == TRUE) {
+                    
+		    CharPtr prefix = WWWGetValueByName(theInfo->info, "DB_DIR_PREFIX");
+		    Char tmpbuf[1024];
+                    
+		    if (prefix) {
+			sprintf(tmpbuf, "%s%c%s", prefix, DIRDELIMCHR, buffer1);
+		    } else {
+			sprintf(tmpbuf, "%s", buffer1);
+		    }
+		    
+		    StringCpy(ptr, tmpbuf);
+		    ptr += StringLen(tmpbuf);
+		    *ptr = ' '; ptr++;
+		} else {
+                    WWWBlastErrMessage(BLASTErrCombination, NULL);
+                    return FALSE;
+		}
+	    }
+	}
+    }
+    
+    if (datalib_found) {
+	ptr--;
+	*ptr = NULLB;
+	theInfo->database = StringSave(buffer);
+    } else {
+        WWWBlastErrMessage(BLASTErrDatalib, NULL);
+	return FALSE;
+    }
+    
+    /* Processing database aliases  */
+    
+    if(StringStr(theInfo->database, "E.coli") != NULL) {
+	MemFree(theInfo->database);
+	theInfo->database = StringSave("ecoli");
+    }
+
+    return TRUE;
+}
+#if defined(NCBI_CLIENT_SERVER) || defined (NCBI_ENTREZ_CLIENT)
+
+static Int4 AccessionToGi (CharPtr string) 
+{
+    Char buffer[32];
+    CharPtr chptr;
+    Int2 version;
+    Int4 gi, index;
+    SeqIdPtr sip;
+    TextSeqIdPtr tsip;
+    PDBSeqIdPtr  psip;
+    long tmplong;
+    Boolean digit;
+
+    for(chptr = string, digit = TRUE; *chptr != NULLB; chptr++) {
+        if(!IS_DIGIT(*chptr)) {
+            digit = FALSE;
+            break;
+        }
+    }
+        
+    if(digit) {
+        if((gi = atol(string)) > 0)
+            return gi;
+    }
+
+    /* all letters in accesion should be upper */
+    string = Nlm_StringUpper(string);
+    
+    gi = 0;
+
+    if((sip = ValNodeNew (NULL)) == NULL)
+        return -1;
+    
+    index = 0; version = 0;
+    while (*string != '\0' && index < 16) {
+        if (*string == '.')
+            break;
+        buffer[index] = *string;
+        string++;
+        index++;
+    }
+
+    buffer[index] = '\0';
+    if (*string == '.' && *(string+1) != '\0') {
+        sscanf((string+1), "%ld", &tmplong);
+        version = (Int2) tmplong;
+    }
+    
+    if((tsip = TextSeqIdNew ()) == NULL)
+        return -1;
+    
+    tsip->accession = StringSave(buffer);
+    tsip->version = version;
+    
+    /* GenBank, EMBL, and DDBJ. */
+    sip->choice = SEQID_GENBANK;
+    sip->data.ptrvalue = (Pointer) tsip;
+    gi = ID1FindSeqId (sip);
+    
+    if (gi == 0) {
+        /* SwissProt. */
+        sip->choice = SEQID_SWISSPROT;
+        gi = ID1FindSeqId (sip);
+    } else {
+        goto retpoint;
+    }
+
+    if (gi == 0) {
+        /* PIR */
+        sip->choice = SEQID_PIR;
+        gi = ID1FindSeqId (sip);
+    } else {
+        goto retpoint;
+    }
+
+    if (gi == 0) {
+        /* PRF */
+        sip->choice = SEQID_PRF;
+        gi = ID1FindSeqId (sip);
+    } else {
+        goto retpoint;
+    }
+
+    if (gi == 0) {
+        /* OTHER, probably 'ref' */
+        sip->choice = SEQID_OTHER;
+        gi = ID1FindSeqId (sip);
+    }
+
+    if(gi != 0)
+        goto retpoint;
+
+    /* OK. We failed to find gi using string as TextSeqId. Now trying
+       last time - with PDBSeqIdPtr */
+
+    if((psip = PDBSeqIdNew()) == NULL)
+        return -1;
+    
+    sip->choice = SEQID_PDB;
+    sip->data.ptrvalue = psip;
+    
+    psip->mol = StringSave(buffer);
+    psip->chain = version;
+
+    gi = ID1FindSeqId (sip);
+
+    SeqIdFree(sip);
+
+ retpoint:
+    TextSeqIdFree(tsip);
+    return gi;
+}
+#endif
+
+#define MAX_NUM_QUERIES 16383 /* == 1/2 INT2_MAX */
+Boolean WWWCreateSearchOptions(WWWBlastInfoPtr theInfo)
+{
+    CharPtr chptr, sequence, outptr;
+    SeqEntryPtr sep;
+    Boolean gapped_set;
+    BLAST_OptionsBlkPtr options;
+    Char tmp[128];
+    Int4 value;
+    Boolean is_megablast = FALSE, mask_lower_case = FALSE;
+    SeqLocPtr query_lcase_mask = NULL;
+    Int4 query_from, query_to;
+    
+    /* PROGRAM */
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "PROGRAM")) != NULL) {
+	theInfo->program = StringSave(chptr);
+    } else {
+        theInfo->program = StringSave("blastn");
+        /*WWWBlastErrMessage(BLASTErrProgram, NULL);
+          return FALSE;*/
+    }
+
+    /* Is it MEGABLAST? */
+
+    if (WWWGetValueByName(theInfo->info, "MEGABLAST") != NULL)
+       is_megablast = TRUE;
+
+    /* Configuration file set program/database relations */
+
+    if((theInfo->blast_config = 
+        BLASTReadConfigFile(theInfo->ConfigFile, theInfo->program)) == NULL) {
+        WWWBlastErrMessage(BLASTConfigFile, NULL);
+	return FALSE;
+    }
+
+    /* DATALIB */
+    if(!WWWParseDatabases(theInfo))
+        return FALSE;
+    
+    /* SEQUENCE or SEQFILE */
+    
+    if((sequence = WWWGetValueByName(theInfo->info, "SEQUENCE")) == NULL)
+       sequence = WWWGetValueByName(theInfo->info, "QUERY");
+
+    if (sequence == NULL || sequence[0] == NULLB) {
+        if((sequence = WWWGetValueByName(theInfo->info, "SEQFILE")) == NULL)
+           sequence = WWWGetValueByName(theInfo->info, "QUERY_FILE");
+        if (sequence == NULL || sequence[0] == NULLB) {
+            WWWBlastErrMessage(BLASTErrNoSequence, NULL);
+            return FALSE;
+        }
+    }
+
+    /* Subsequence coordinates */
+    if ((chptr = WWWGetValueByName(theInfo->info, "QUERY_FROM")) != NULL
+         && *chptr != NULLB) {
+       query_from = MAX(atoi(chptr), 0);
+    } else {
+       query_from = 0;
+    }
+
+    if ((chptr = WWWGetValueByName(theInfo->info, "QUERY_TO")) != NULL
+         && *chptr != NULLB) {
+       query_to = MAX(atoi(chptr), -1);
+    } else {
+       query_to = -1;
+    }
+        
+    theInfo->align_type = BlastGetTypes(theInfo->program, &theInfo->query_is_na, &theInfo->db_is_na);
+#if defined(NCBI_CLIENT_SERVER) || defined (NCBI_ENTREZ_CLIENT)
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "INPUT_TYPE")) != NULL && 
+       !StringNICmp(chptr, "Accession", 9)) {
+
+        Int4 gi, number, title_length, id_length, query_num = 0;
+        CharPtr accession, new_defline;
+        BioseqPtr bsp_tmp, query_bsp;
+        SeqIdPtr sip;
+        ObjectIdPtr  oid;
+        SeqPortPtr spp;
+        Int2 retval, buf_length=512;
+        Uint1 buf[512];
+        Char tmp[255];
+        Boolean first_query = TRUE;
+        Char delimiters[7];
+
+	/* This is request by Accession/GI - asking ID */
+        
+        if (!ID1BioseqFetchEnable("web-blasts", TRUE)) {
+            WWWBlastErrMessage(BLASTEntrez, NULL);
+	    return FALSE;
+        }
+        
+	chptr = sequence;
+        theInfo->query_slp = NULL;
+        StrCpy(delimiters, " \t\n,;\r");
+
+        while (outptr = StringTokMT(chptr, delimiters, &chptr)) {
+
+           accession = outptr;
+
+           /* Strip off non-alphanumerics, except for '_' (used in SP) and '.' (soon to be used by  the collaboration. */
+           while (IS_ALPHANUM(*outptr) || *outptr == '_' || *outptr == '.')
+              outptr++;
+           *outptr = NULLB; 
+           
+           sip = NULL;
+           gi = AccessionToGi(accession);
+           
+           if (gi > 0) {
+              ValNodeAddInt(&sip, SEQID_GI, gi);
+           } else {
+              WWWBlastErrMessageEx(BLASTEntrez, NULL, accession);
+              if (!theInfo->query_slp && !chptr) 
+                 return FALSE;
+              else continue;
+           }	
+           
+           /* If id is not found - it is not found - ID1 is down? */
+           
+           if((bsp_tmp = BioseqLockById(sip)) == NULL) {
+              WWWBlastErrMessageEx(BLASTEntrez, NULL, accession);
+              if (!theInfo->query_slp && !chptr) 
+                 return FALSE;
+              else continue;
+           }
+           
+           if (ISA_na(bsp_tmp->mol) != theInfo->query_is_na) {
+              WWWBlastErrMessageEx(BLASTErrAccType, NULL, accession);
+              if (!theInfo->query_slp && !chptr) 
+                 return FALSE;
+              else continue;
+           }
+           
+           query_bsp = BioseqNew();
+           query_bsp->length = bsp_tmp->length;
+           query_bsp->mol = bsp_tmp->mol;
+           query_bsp->repr = Seq_repr_raw;
+           query_bsp->seq_data = BSNew(query_bsp->length);
+           
+           if (ISA_na(query_bsp->mol)) {
+              spp = SeqPortNew(bsp_tmp, 0, -1, Seq_strand_plus, 
+                               Seq_code_iupacna);
+              query_bsp->seq_data_type = Seq_code_iupacna;
+           } else {
+              spp = SeqPortNew(bsp_tmp, 0, -1, Seq_strand_unknown, 
+                               Seq_code_ncbieaa);
+              query_bsp->seq_data_type = Seq_code_ncbieaa;
+           }
+           
+           SeqPortSet_do_virtual(spp, TRUE);
+           number = 0;
+           while (number < query_bsp->length) {
+              retval = SeqPortRead(spp, buf, buf_length);
+              if (retval < 0)
+                 continue;
+              if (retval == 0)
+                 break;
+              BSWrite(query_bsp->seq_data, buf, retval);
+              number += retval;
+           }
+           
+           SeqPortFree(spp);
+           
+           title_length = StringLen(BioseqGetTitle(bsp_tmp));
+           SeqIdWrite(bsp_tmp->id, tmp, PRINTID_FASTA_LONG, 255);
+           id_length = StringLen(tmp);
+           title_length += id_length;
+           title_length +=3;
+           new_defline = (CharPtr) MemNew(title_length*sizeof(Char));
+           StringCpy(new_defline, tmp);
+           *(new_defline+id_length) = ' ';
+           StringCpy(new_defline+id_length+1, BioseqGetTitle(bsp_tmp)); 
+           *(new_defline+title_length-1) = NULLB;
+           query_bsp->descr = ValNodeAddStr(NULL, Seq_descr_title, 
+                                            new_defline);
+           query_bsp->id = ValNodeNew(NULL);
+           oid = ObjectIdNew();
+           query_num++;
+           oid->str = (CharPtr) Malloc(6);
+           sprintf(oid->str, "%d", query_num);
+           query_bsp->id->choice = SEQID_LOCAL;
+           query_bsp->id->data.ptrvalue = (Pointer) oid;
+        
+           SeqMgrDeleteFromBioseqIndex(bsp_tmp);
+           
+           BioseqUnlock(bsp_tmp);
+           
+           BioseqPack(query_bsp);
+           if (first_query) {
+              theInfo->query_bsp = query_bsp;
+              first_query = FALSE;
+           }
+        
+           if (query_from == 0 && query_to == -1) {
+              ValNodeAddPointer(&theInfo->query_slp, SEQLOC_WHOLE,
+                 SeqIdSetDup(SeqIdFindBest(query_bsp->id, SEQID_GI)));
+           } else {
+              if (query_to == -1 || query_to > query_bsp->length)
+                 query_to = query_bsp->length - 1;
+              theInfo->query_slp = 
+                 SeqLocIntNew(query_from, query_to, Seq_strand_both, 
+                    SeqIdSetDup(SeqIdFindBest(query_bsp->id, SEQID_GI)));
+              /* Only one query permitted if subsequence coordinates are
+                 provided */
+              break;
+           }
+        }
+        
+        ID1BioseqFetchDisable();
+    }
+#endif
+
+    /* LCASE_MASK */
+    if (WWWGetValueByName(theInfo->info, "LCASE_MASK") != NULL)
+       mask_lower_case = TRUE;
+
+
+    /* Creating Bioseq */
+        
+    if (theInfo->query_bsp == NULL) {
+	  Int4 num_queries;
+	  BioseqPtr query_bsp = NULL;
+	  SeqLocPtr last_mask, mask_slp;
+	  Int2 ctr = 1;
+	  Char prefix[2];
+	  
+          outptr = NULL;
+	  StrCpy(prefix, "");
+	  SeqMgrHoldIndexing(TRUE);
+	  mask_slp = last_mask = NULL;
+	  num_queries = 0;
+	  while ((sep=FastaToSeqBuffForDb(sequence, &outptr,
+					  theInfo->query_is_na, NULL,
+					  theInfo->believe_query, 
+                                          prefix, &ctr, &mask_slp)) != NULL) {
+             sequence = outptr;
+	     if (mask_slp) {
+                if (!mask_lower_case)
+                   SeqLocFree(mask_slp);
+		else if (!last_mask)
+		   query_lcase_mask = last_mask = mask_slp;
+		else {
+		   last_mask->next = mask_slp;
+		   last_mask = last_mask->next;
+		}
+		mask_slp = NULL;
+	     }
+	     query_bsp = NULL;
+	     if (theInfo->query_is_na) 
+		SeqEntryExplore(sep, &query_bsp, FindNuc);
+	     else
+		SeqEntryExplore(sep, &query_bsp, FindProt);
+	     
+	     if (query_bsp == NULL) {
+		ErrPostEx(SEV_FATAL, 0, 0, "Unable to obtain bioseq\n");
+		return 2;
+	     }
+	     num_queries++;
+	     if (num_queries > MAX_NUM_QUERIES) {
+		WWWBlastErrMessage(BLASTOptionStr, 
+				   "Maximal number of queries exceeded. At most 16383 are allowed");
+		break;
+	     }
+	     if (!theInfo->query_slp) /* I.e. if first query */
+		theInfo->query_bsp = query_bsp;
+
+             if (query_from == 0 && query_to == -1) {
+                ValNodeAddPointer(&theInfo->query_slp, SEQLOC_WHOLE,
+                   SeqIdSetDup(SeqIdFindBest(query_bsp->id, SEQID_GI)));
+             } else {
+                if (query_to == -1 || query_to > query_bsp->length)
+                   query_to = query_bsp->length - 1;
+                theInfo->query_slp = 
+                   SeqLocIntNew(query_from, query_to, Seq_strand_both, 
+                      SeqIdSetDup(SeqIdFindBest(query_bsp->id, SEQID_GI)));
+                /* Only one query permitted if subsequence coordinates are
+                   provided */
+                break;
+             }
+	  }
+	  SeqMgrHoldIndexing(FALSE);
+    } else if (is_megablast && !theInfo->query_slp) {
+       if (query_from == 0 && query_to == -1) {
+          ValNodeAddPointer(&theInfo->query_slp, SEQLOC_WHOLE,
+             SeqIdSetDup(SeqIdFindBest(theInfo->query_bsp->id, SEQID_GI)));
+       } else {
+          if (query_to == -1 || query_to > theInfo->query_bsp->length)
+             query_to = theInfo->query_bsp->length - 1;
+          theInfo->query_slp = 
+             SeqLocIntNew(query_from, query_to, Seq_strand_both, 
+                SeqIdSetDup(SeqIdFindBest(theInfo->query_bsp->id, SEQID_GI)));
+       }
+    }
+       
+    /* The last check of Bioseq - if length of sequence too small ? */
+    
+    if(theInfo->query_bsp == NULL || 
+       theInfo->query_bsp->length <= 0) {
+        WWWBlastErrMessage(BLASTFastaToSE, NULL);
+        return FALSE;
+    }
+    
+    /* This will prevent from incorrect formating in case when input
+       sequence has valid SeqId, but in fact this SeqId do not correspond
+       to the real sequence  - XXX */
+
+    if(!theInfo->believe_query)
+        theInfo->fake_bsp = BlastMakeFakeBioseq(theInfo->query_bsp, NULL);
+    else
+        theInfo->fake_bsp = theInfo->query_bsp;
+    
+    /* OVERVIEW */
+    
+    if (WWWGetValueByName(theInfo->info, "OVERVIEW") != NULL ||
+        WWWGetValueByName(theInfo->info, "SHOW_OVERVIEW") != NULL)
+        theInfo->show_overview = TRUE;
+
+    /* UNGAPPED_ALIGNMENT */
+    gapped_set = TRUE;
+    if(WWWGetValueByName(theInfo->info, "UNGAPPED_ALIGNMENT") != NULL)
+	gapped_set = FALSE;
+
+    if((options = BLASTOptionNewEx(theInfo->program, gapped_set, is_megablast)) == NULL) {
+        WWWBlastErrMessage(BLASTErrOptions, NULL);
+	return FALSE; 
+    }
+    
+    if (is_megablast) {
+       options->query_lcase_mask = query_lcase_mask;
+       if((chptr = WWWGetValueByName(theInfo->info, "WORD_SIZE")) != NULL &&
+          StringStr(chptr, "default") == NULL) {
+          options->wordsize = atoi(chptr);
+       }
+       /* Mega BLAST with no traceback (endpoints only)? */
+       if (WWWGetValueByName(theInfo->info, "ENDPOINTS") != NULL)
+          options->no_traceback = TRUE;
+       if ((chptr = WWWGetValueByName(theInfo->info, "PERC_IDENT")) != NULL && 
+           StringStr(chptr, "default") == NULL)
+          options->perc_identity = (FloatLo) atof(chptr);
+    }
+
+    theInfo->options = options;
+
+    /* Set default values for matrix and gap parameters */
+    BLASTOptionSetGapParams (options, NULL, 0, 0);
+    
+    /* Read MAT_PARAM if set */
+    
+    if(StringICmp("blastn", theInfo->program) && 
+       (chptr = WWWGetValueByName(theInfo->info, "MAT_PARAM")) != NULL) {
+        Char    matrixname[64];
+        Int4    opencost, extendedcost;
+        /* Get matrix name and gap costs */
+        if (chptr[1] != '-' || chptr[2] != '-') {
+            sscanf(chptr, "%s\t %d\t %d", matrixname, &opencost, 
+                   &extendedcost);
+            /* set the parameters */
+            options->gap_open  = opencost;
+            options->gap_extend  = extendedcost;
+            if (options->matrix)
+                MemFree(options->matrix);
+            options->matrix = StringSave(matrixname);
+        }
+    } 
+
+    if((chptr = WWWGetValueByName(theInfo->info, "GAP_OPEN")) != NULL &&
+	    StringStr(chptr, "default") == NULL) {
+	options->gap_open = atoi(chptr);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, "GAP_EXTEND")) != NULL &&
+	    StringStr(chptr, "default") == NULL) {
+	options->gap_extend = atoi(chptr);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, "GAP_VALUES")) != NULL &&
+	    StringStr(chptr, "default") == NULL) {
+	sscanf(chptr, "%d,%d", &options->gap_open, &options->gap_extend);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, "X_DROPOFF")) != NULL &&
+	    StringStr(chptr, "default") == NULL) {
+	options->gap_x_dropoff = atoi(chptr);
+    }
+
+    if (!StringICmp(theInfo->program, "blastn")) {
+       if (options->perc_identity >= 95.0 || options->perc_identity == 0.0) {
+          options->reward = 1;
+          options->penalty = -3;
+       } else if (options->perc_identity >= 85.0) {
+          options->reward = 1;
+          options->penalty = -2;
+       } else if (options->perc_identity >= 80.0) {
+          options->reward = 2;
+          options->penalty = -3;
+       } else if (options->perc_identity >= 75.0) {
+          options->reward = 4;
+          options->penalty = -5;
+       } else if (options->perc_identity >= 60.0) {
+          options->reward = 2;
+          options->penalty = -2;
+       }
+    }
+
+    /* The discontiguous word options */
+    if ((chptr = WWWGetValueByName(theInfo->info, "TEMPLATE_LENGTH")) != NULL)
+       options->mb_template_length = atoi(chptr);
+
+    if (WWWGetValueByName(theInfo->info, "TWO_HITS") != NULL)
+       options->window_size = 40;
+    if ((chptr = WWWGetValueByName(theInfo->info, "TEMPLATE_TYPE")) != NULL)
+       options->mb_disc_type = (MBDiscWordType) atoi(chptr);
+
+    /* Set the gap penalties depending on the percent identity cutoff, if
+       the discontiguous word approach is used. Also make sure non-greedy
+       dynamic programming algorithm is used for gapped extension */
+    if (options->mb_template_length > 0 && options->wordsize <= 12 && 
+        options->wordsize >= 11 && options->perc_identity < 90.0) {
+       options->mb_use_dyn_prog = TRUE;
+       if (options->perc_identity >= 85.0) {
+          options->gap_open = 4;
+          options->gap_extend = 1;
+       } else if (options->perc_identity >= 80.0) {
+          options->gap_open = 5;
+          options->gap_extend = 2;
+       } else if (options->perc_identity >= 75) {
+          options->gap_open = 7;
+          options->gap_extend = 2;
+       } else if (options->perc_identity >= 60) {
+          options->gap_open = 3;
+          options->gap_extend = 1;
+       }
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, "GAP_SIZE")) != NULL &&
+	    StringStr(chptr, "default") == NULL) {
+	options->gap_size = atoi(chptr);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "WINDOW_SIZE")) != NULL &&
+	    StringStr(chptr, "default") == NULL) {
+	options->window_size = atoi(chptr);
+    }
+
+    /* For BLASTX we could set genetic code */
+
+    if (!StringICmp(theInfo->program, "blastx")) {
+        BioSourcePtr source;
+        
+	options->genetic_code = 1;
+
+	if((chptr = WWWGetValueByName(theInfo->info, 
+		"GENETIC_CODE")) != NULL &&
+		(StringStr(chptr, "default") == NULL)) {
+	    chptr = StringChr(chptr, '(');
+	    sscanf(chptr, "(%d", &value);
+	    if(value != 0) {
+		options->genetic_code = value; 
+
+		source = BioSourceNew();
+		source->org = OrgRefNew();
+		source->org->orgname = OrgNameNew();
+		source->org->orgname->gcode = options->genetic_code;
+		ValNodeAddPointer(&theInfo->query_bsp->descr, 
+			Seq_descr_source, source);
+	    }
+	}
+    }
+
+    /* For BLASTX we could set genetic code */
+
+    if (!StringICmp(theInfo->program, "blastx")) {
+	if((chptr = WWWGetValueByName(theInfo->info, "OOF_ALIGN")) != NULL) {
+            options->is_ooframe = TRUE;
+            options->shift_pen = atoi(chptr);
+
+            if(options->shift_pen == 0) {
+                options->is_ooframe = FALSE;
+            }
+        }
+    }
+
+    /* For TBLASTN and TBLASTX we could set DB_GENETIC_CODE */
+
+    if (!StringICmp(theInfo->program, "tblastn") || 
+        !(StringICmp(theInfo->program, "tblastx"))) {
+	options->db_genetic_code = 1;
+	if((chptr = WWWGetValueByName(theInfo->info, 
+                                      "DB_GENETIC_CODE")) != NULL &&
+           (StringStr(chptr, "default") == NULL)) {
+	    chptr = StringChr(chptr, '(');
+	    sscanf(chptr, "(%d", &value);
+	    if(value != 0) {
+		options->db_genetic_code = value; 
+	    }      
+	}
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "THRESHOLD_2")) != NULL &&
+	    (StringStr(chptr, "default") == NULL)) {
+	options->threshold_second = atoi(chptr);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "REQUIRED_START")) != NULL &&
+	    StringStr(chptr, "default") != NULL) {
+	options->required_start = atoi(chptr);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "REQUIRED_END")) != NULL &&
+	    StringStr(chptr, "default") != NULL) {
+	options->required_end = atoi(chptr);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "DROPOFF_1")) != NULL &&
+	    (StringStr(chptr, "default") == NULL)) {
+	options->dropoff_1st_pass = atof(chptr);
+    }
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "CUTOFF")) != NULL &&
+	    (StringStr(chptr, "default") == NULL)) {
+	options->cutoff_s = atof(chptr);
+    }
+
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "DROPOFF_2")) != NULL &&
+	    (StringStr(chptr, "default") == NULL)) {
+	options->dropoff_2nd_pass = atof(chptr);
+    }
+
+    /* MATRIX: */
+    if ((chptr = WWWGetValueByName(theInfo->info, "MATRIX")) == NULL)
+       chptr = WWWGetValueByName(theInfo->info, "MATRIX_NAME");
+
+    if(chptr != NULL && (StringStr(chptr, "default") == NULL)) {
+	options->matrix = StringSave(chptr);
+    }
+
+    /* EXPECT */
+
+    options->expect_value  = DEFAULT_EXPECT;
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "EXPECT")) != NULL &&
+	    StringStr(chptr, "default") == NULL) {
+	options->expect_value = atof(chptr);
+    }
+
+    /* NUMBER OF BITS: */
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+	    "NUM_OF_BITS")) != NULL &&
+	    (StringStr(chptr, "default") == NULL)) {
+	options->number_of_bits = atof(chptr);
+    }
+
+    /* RPSBLAST */
+
+    if (WWWGetValueByName(theInfo->info, "RPSBLAST") != NULL)
+        options->is_rps_blast = TRUE;
+
+    /* ENTREZ_QUERY */
+    
+    if ((chptr = WWWGetValueByName(theInfo->info, "ENTREZ_QUERY")) != NULL) {
+        options->entrez_query = StringSave(chptr);
+    
+#if defined(NCBI_CLIENT_SERVER) || defined (NCBI_ENTREZ_CLIENT)
+        {{
+            Int4 i;
+            Int4Ptr uids;
+
+            theInfo->gi_list_total = 
+                BLASTGetUidsFromQuery(chptr, &uids, theInfo->db_is_na, FALSE, 0);
+
+            if(theInfo->gi_list_total > 0) {
+
+                theInfo->gi_list = MemNew(theInfo->gi_list_total*sizeof(BlastDoubleInt4));
+                for(i = 0; i < theInfo->gi_list_total; i++)
+                    theInfo->gi_list[i].gi = uids[i];
+            }
+        }}
+#endif
+    }
+    /* ----------------------------------- */
+
+    /* Number of CPU to use in BLAST Search: */
+
+    if(theInfo->blast_config->num_cpu != 0)
+        options->number_of_cpus = theInfo->blast_config->num_cpu;
+    else
+        options->number_of_cpus = NUM_CPU_TO_USE;
+
+    /* CPU time limit. */
+    
+    options->cpu_limit = DEFAULT_CPU_LIMIT;
+
+    /* FILTER: */
+
+
+    options->filter = FILTER_NONE;
+
+    if(WWWGetMethod(theInfo->info) == WWW_GET ||
+	    (chptr = WWWGetValueByName(theInfo->info, "FSET")) != NULL) {
+	if (!StringICmp(theInfo->program, "blastn")) {
+	    options->filter = FILTER_DUST;
+	} else {
+	    options->filter = FILTER_SEG;
+	}
+    }
+    
+    {
+        Char	tmpbuf[4096];
+        /* Filter settings */
+	int	i, num_entries = WWWGetNumEntries(theInfo->info);
+        
+	StringCpy(tmpbuf, "");
+
+	for(i = 0; i < num_entries; i++) {
+	    if((chptr = WWWGetNameByIndex(theInfo->info, i)) != NULL && 
+		    !StringICmp(chptr, "FILTER")) {
+
+		chptr = WWWGetValueByIndex(theInfo->info, i);
+		/* add the filter */
+		StringCat(tmpbuf, chptr);
+		StringCat(tmpbuf, ";");
+	    }
+	}
+	options->filter_string = StringSave(tmpbuf);
+    }
+
+    /* DESCRIPTIONS: */
+
+    theInfo->number_of_descriptions = DEFAULT_DESCRIPTIONS;
+
+    if((chptr = WWWGetValueByName(theInfo->info, 
+                                  "DESCRIPTIONS")) != NULL && 
+       StringStr(chptr, "default") == NULL) {
+	theInfo->number_of_descriptions = atoi(chptr);
+    }
+    
+    /* ALIGNMENTS */
+    theInfo->number_of_alignments = DEFAULT_ALIGNMENTS;
+
+    if((chptr = WWWGetValueByName(theInfo->info, "ALIGNMENTS")) != NULL &&
+       StringStr(chptr, "default") == NULL) {
+	theInfo->number_of_alignments = atoi(chptr);  
+    }
+    
+    /* Now processing OTHER_ADVANCED_OPTIONS */
+    
+    if((chptr = WWWGetValueByName(theInfo->info, 
+                                  "OTHER_ADVANCED")) != NULL) {
+        CharPtr ErrorMessage = NULL;
+        int other_adv_descriptions = -1, other_adv_alignments = -1;
+
+        parse_blast_options(options, chptr, &ErrorMessage, NULL,
+                            &other_adv_descriptions, &other_adv_alignments);
+
+        if (ErrorMessage) {
+            WWWBlastErrMessage(BLASTOptionStr, ErrorMessage);
+	    return FALSE;
+	}
+        if (other_adv_alignments != -1) { /* if defined */
+           theInfo->number_of_alignments = other_adv_alignments;
+        }
+
+        if (other_adv_descriptions != -1) { /* if defined */
+           theInfo->number_of_descriptions = other_adv_descriptions;
+        }
+    }
+
+    /* HITLIST_SIZE: */
+    
+    options->hitlist_size = MAX(theInfo->number_of_descriptions, 
+                                theInfo->number_of_alignments);
+    
+    options->perform_culling = FALSE;
+
+    /* Parameters for Smith-Waterman BLAST */
+
+    /* TWEAK_PARAMETERS */
+    
+    if (WWWGetValueByName(theInfo->info, "TWEAK_PARAMETERS") != NULL || 
+        WWWGetValueByName(theInfo->info, "COMPOSITION_BASED_STATISTICS") 
+        != NULL)
+        options->tweak_parameters = TRUE;
+
+    /* Adjustment of expect value and hitlist size */
+    if (options->tweak_parameters) {
+        options->hitlist_size *= 2; /*allows for extra matches*/
+        options->original_expect_value = 
+            options->expect_value;
+        if (options->expect_value < 0.1) {
+            options->expect_value = 
+                MIN(0.1, 10 * options->expect_value);
+        }
+    }
+    
+    /* SMITH_WATERMAN */
+    
+    if (WWWGetValueByName(theInfo->info, "SMITH_WATERMAN") != NULL)
+        options->smith_waterman = TRUE;
+
+    /* Some values for PSI-Blast */
+    value = 0;
+    if((chptr = WWWGetValueByName(theInfo->info, "STEP_NUMBER")) != NULL)
+	value = atoi(chptr);
+    
+    sprintf(tmp, "PSI_BEGIN%d", value-1);
+    
+    if((chptr = WWWGetValueByName(theInfo->info, tmp)) != NULL)
+	options->required_start = atoi(chptr) - 1;
+    
+    sprintf(tmp, "PSI_END%d", value-1);
+    if((chptr = WWWGetValueByName(theInfo->info, tmp)) != NULL)
+	options->required_end = atoi(chptr) - 1;    
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "E_THRESH")) != NULL)
+	options->ethresh = atof(chptr);
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "PHI_BLAST")) != NULL) {
+	theInfo->is_phi_blast = TRUE;
+        options->number_of_cpus = 1;
+    }
+    
+    /* ------------------------ */
+
+    /* ALIGNMENT VIEWS */
+    
+    if((chptr = WWWGetValueByName(theInfo->info, 
+                                  "ALIGNMENT_VIEW")) != NULL &&
+       StringStr(chptr, "default") == NULL) {
+	theInfo->align_view = (BLASTAlignView) atoi(chptr);
+        
+        if(theInfo->align_view == BlastXML) {
+            theInfo->xml_output = TRUE;
+        }
+    }
+
+    if (WWWGetValueByName(theInfo->info, "XML_OUTPUT") != NULL)
+	theInfo->xml_output = TRUE;
+
+    if(options->is_ooframe) {
+        theInfo->xml_output = FALSE;
+        theInfo->align_view = Pairwise;
+    }
+
+    if (WWWGetValueByName(theInfo->info, "NCBI_GI") != NULL)
+	theInfo->show_gi = TRUE;
+    
+    if (WWWGetValueByName(theInfo->info, "TAX_BLAST") != NULL)
+        theInfo->show_tax_blast = TRUE;
+    
+    /* COLOR_SCHEMA */
+    if((chptr = WWWGetValueByName(theInfo->info, "COLOR_SCHEMA")) != NULL &&
+       StringStr(chptr, "No color schema") == NULL) {
+	theInfo->color_schema = atoi(chptr);  
+    }
+    /* Now seting print and align options for BLAST output printing */
+
+    theInfo->print_options = 0;
+    theInfo->align_options = 0;
+    theInfo->align_options += TXALIGN_COMPRESS;
+    theInfo->align_options += TXALIGN_END_NUM;
+
+    if (StringICmp("blastx", theInfo->program) == 0) {
+        theInfo->align_options += TXALIGN_BLASTX_SPECIAL;
+    }
+
+    if (theInfo->show_gi) {
+        theInfo->align_options += TXALIGN_SHOW_GI;
+        theInfo->print_options += TXALIGN_SHOW_GI;
+    }
+
+    theInfo->print_options += TXALIGN_SHOW_LINKOUT;
+
+    if (!gapped_set)
+        theInfo->print_options += TXALIGN_SHOW_NO_OF_SEGS;
+    
+    if (theInfo->align_view != Pairwise) {
+        theInfo->align_options += TXALIGN_MASTER;
+        if (theInfo->align_view == QueryAnchoredIdent || 
+            theInfo->align_view == FlatQueryAnchoredIdent)
+            theInfo->align_options += TXALIGN_MISMATCH;
+        if (theInfo->align_view == FlatQueryAnchoredIdent || 
+            theInfo->align_view == FlatQueryAnchoredNoIdent || 
+            theInfo->align_view == FlatQueryAnchoredBluntEnd)
+            theInfo->align_options += TXALIGN_FLAT_INS;
+        if (theInfo->align_view == QueryAnchoredBluntEnd || 
+            theInfo->align_view == FlatQueryAnchoredBluntEnd)
+            theInfo->align_options += TXALIGN_BLUNT_END;
+    } else {
+        theInfo->align_options += TXALIGN_MATRIX_VAL;
+        theInfo->align_options += TXALIGN_SHOW_QS;
+    }
+    
+    /* Always HTML in WWW case */
+#if 1    
+    theInfo->align_options += TXALIGN_HTML;
+    theInfo->print_options += TXALIGN_HTML;
+#endif    
+    return TRUE;
+}
+
+Boolean WWWValidateOptions(WWWBlastInfoPtr theInfo)
+{
+    ValNodePtr error_return=NULL;
+    BlastErrorMsgPtr error_msg;
+    CharPtr msg = NULL;
+
+    if(theInfo == NULL || theInfo->options == NULL)
+	return FALSE;
+    
+    if(BLASTOptionValidateEx(theInfo->options, theInfo->program, 
+                             &error_return) != 0) {
+	if (error_return) {
+	    error_msg = (BlastErrorMsgPtr) error_return->data.ptrvalue;
+            msg = error_msg->msg;
+	}
+        WWWBlastErrMessage(BLASTErrOptions, msg);
+
+	return FALSE;
+    }
+    return TRUE;
+}
+
+/* Used for PSI/PHI Blast searches */
+
+static Int1 S62ToInt(Uint1 ch)
+{
+    if(isupper(ch)) /* negative value */
+	return(64 - ch);
+    else if (isdigit(ch)) /* positive less than 10 */
+	return(ch - 48); 
+    else if (!isupper(ch)) /* positive more or eq  10 */
+	return(ch - 87);
+    return 0;
+}
+
+static Uint1 IntTo62S(Int1 value)
+{
+    if(value < 0)
+	return(64-value);
+    else if (value < 10)
+	return(value + 48); 
+    else if (value < 36)
+	return(value + 87);
+    return 0;
+}
+
+static Int4 BLASTCharTo4bits(Char ch)
+{
+    if(ch != '0')
+        ch = ch;
+    if ((ch >= 'A') && (ch <= 'F'))
+        return (((ch - 'A') + 10));
+    else if ((ch >= '0') && (ch <= '9'))
+        return ((ch - '0'));
+    else
+        return (Int4)(-1);
+}
+
+static Char BLAST4bitsToChar(int value)
+{
+    if (value < 10)
+        return (Char)(value + '0');
+    else
+        return (Char)(value - 10 + 'A');
+}
+
+static Nlm_FloatHi **BLASTDecodePosFreqs(CharPtr CHARPosFreqs,
+                                         Int4 length, Int4 size)
+{
+    Nlm_FloatHi **posFreqs;
+    register Int4 i, j, k = 0, l;
+    Nlm_FloatLo fvalue;
+    Uint4 ivalue = 0;
+    
+    if(CHARPosFreqs == NULL || CHARPosFreqs[0] == NULLB)
+	return NULL;
+    
+    posFreqs = (Nlm_FloatHi **) MemNew(sizeof(Nlm_FloatHi *)*(length+1));
+    
+    for(i = 0; i <= length; i++)
+	posFreqs[i] = (Nlm_FloatHi *) MemNew(sizeof(Nlm_FloatHi)*size);
+    
+    for(i = 0, k = 0; i <= length; i++) {
+	for(j =0; j < size; j++) {
+            for(l = 0; l < 8; l++, k++) {
+                ivalue += (BLASTCharTo4bits(CHARPosFreqs[k]) << (l * 4));
+                /* ivalue = ivalue << 4; */
+            }
+            
+            MemCpy(&fvalue, &ivalue, 4);
+            posFreqs[i][j] = (Nlm_FloatHi) fvalue; /* 4 bytes into 8 bytes */
+            ivalue = 0;
+	}
+    }
+    return posFreqs;
+}
+
+static Int4Ptr PNTR Decode62Matrix(CharPtr Matrix62, Int4 length, Int4 size)
+{
+    Int4Ptr PNTR posMatrix;
+    register Int4 i, j, k = 0;
+
+    if(Matrix62 == NULL || Matrix62[0] == NULLB)
+	return NULL;
+
+    posMatrix = (Int4Ptr PNTR) MemNew(sizeof(Int4Ptr)*(length+1));
+
+    for(i = 0; i <= length; i++)
+	posMatrix[i] = (Int4Ptr) MemNew(sizeof(Int4Ptr)*size);
+
+    for(i = 0; i <= length; i++) {
+	for(j =0; j < size; j++) {
+	    if(Matrix62[k] == 'z')
+		posMatrix[i][j] = BLAST_SCORE_MIN;
+	    else if (Matrix62[k] == 'Z')
+		posMatrix[i][j] = BLAST_SCORE_MAX; 
+	    else
+		posMatrix[i][j]= S62ToInt(Matrix62[k]);
+	    k++;
+	}
+    }
+    return posMatrix;
+}
+static CharPtr BLASTEncodePosFreqs(Nlm_FloatHi **posFreqs, 
+                                   Int4 length, Int4 size)
+{    
+    Int4 i, j, k=0, ivalue, fmask, l;
+    CharPtr CHARPosFreqs;
+    Nlm_FloatLo fvalue;
+    
+    /* So... size of the buffer will be eq. to number of elements
+       in the posFreqs matrix times 8:  2 characters for every byte */
+    CHARPosFreqs = (CharPtr) MemNew((length+1)*(size+1)*sizeof(Nlm_FloatLo)*2);
+    
+    for(i = 0, k = 0; i <= length; i++) {
+	for(j =0; j < size; j++) {
+	    fvalue = (Nlm_FloatLo) posFreqs[i][j]; /* truncation to 4 bytes */
+            fmask = 0xF;       /* 4 bits */
+            if(fvalue != 0.0)
+                j=j;
+            
+            MemCpy(&ivalue, &fvalue, 4);
+            for(l = 0; l < 8; l++, k++) {
+                CHARPosFreqs[k] = BLAST4bitsToChar((ivalue & fmask) >> l * 4);
+                fmask = fmask << 4;
+            }
+	}
+    }
+
+    return CHARPosFreqs;
+}
+static CharPtr Encode62Matrix(Int4Ptr PNTR posMatrix, Int4 length, Int4 size)
+{
+    register Int4 i, j, k=0;
+    CharPtr Matrix62;
+
+    Matrix62 = (CharPtr) MemNew((length+1)*size+1);
+
+    for(i = 0; i <= length; i++) {
+	for(j =0; j < size; j++) {
+
+	    if(posMatrix[i][j] < -26)
+		Matrix62[k] = 'z';
+	    else if (posMatrix[i][j] > 35)
+		Matrix62[k] = 'Z';
+	    else
+		Matrix62[k] = IntTo62S(posMatrix[i][j]);
+
+	    k++;
+	}
+    }
+    return Matrix62;
+}
+
+void BLASTPrintDataFree(BLASTPrintDataPtr data)
+{
+    GIListPtr glp, glp_next;
+    ValNodePtr vnp;
+
+    if(data == NULL)
+	return;
+
+    TxDfDbInfoDestruct(data->dbinfo);
+    MemFree(data->ka_params);
+    MemFree(data->ka_params_gap);
+    MemFree(data->buffer);
+    ValNodeFreeData(data->info_vnp);
+    
+    if(data->psidata != NULL) {
+        MemFree(data->psidata->matrix62);
+        MemFree(data->psidata->CHARPosFreqs);
+
+        for(glp = data->psidata->PrevCheckedGIs; glp != NULL; glp = glp_next) {
+            glp_next = glp->next;
+            MemFree(glp);
+        }
+
+        for(glp = data->psidata->PrevGoodGIs; glp != NULL; glp = glp_next) {
+            glp_next = glp->next;
+            MemFree(glp);
+        }
+        MemFree(data->psidata);
+    }
+    
+    if(data->seqalign != NULL)
+        SeqAlignSetFree(data->seqalign);
+    
+    SeqLocFree(data->seqloc);
+    
+    for(vnp = data->vnp; vnp != NULL; vnp=vnp->next) {
+        SeqAlignSetFree((SeqAlignPtr) vnp->data.ptrvalue);
+    }
+    
+    ValNodeFree(data->vnp);
+    
+    MemFree(data);
+    return;
+}
+
+/* We got seqalign list, now divide it into two lists:
+   the first one will contain alignments with Evalue
+   better than threshold, other worse than threshold
+*/
+
+Boolean 
+SplitSeqAlign(SeqAlignPtr seqalign, SeqAlignPtr *GoodSeqAlignment_ptr, 
+              SeqAlignPtr *BadSeqAlignment_ptr, SeqAlignPtr *lastGood_ptr, 
+              Int2Ptr *marks_ptr, Int2Ptr countBad_ptr, 
+              Int2Ptr countGood_ptr, Nlm_FloatHi ethresh_old)
+{
+    
+    Boolean first_time;
+    SeqIdPtr last_id, subject_id;
+    SeqAlignPtr         gsl, seqalign_var, last_seqalign;
+    SeqAlignPtr		BadSeqAlignments, GoodSeqAlignments, lastGood = NULL;
+    Nlm_FloatHi         bit_score, evalue;
+    Int2Ptr		marks;
+    Int2		countGood, countBad;
+    Int4                number, score;
+
+    last_id = NULL;
+    first_time = TRUE;
+    GoodSeqAlignments = seqalign_var = seqalign;
+    
+    BadSeqAlignments = NULL;
+    while (seqalign_var) {
+	subject_id = SeqIdDup(TxGetSubjectIdFromSeqAlign(seqalign_var));
+	if (last_id == NULL || SeqIdComp(subject_id, last_id) == SIC_NO) {
+            SeqIdSetFree(last_id);
+            last_id = subject_id;
+            GetScoreAndEvalue(seqalign_var, &score, &bit_score, &evalue, &number);
+            if (evalue > ethresh_old) {
+                if (first_time == TRUE) {
+                    GoodSeqAlignments = NULL;
+                    lastGood = NULL;
+                    last_seqalign = NULL;	/* split the good and bad lists. */
+                } else {
+                    lastGood = last_seqalign;
+                    last_seqalign->next = NULL;	/* split the good and bad lists. */
+                }
+                BadSeqAlignments = seqalign_var;
+                break;	
+            }
+	} else {
+            SeqIdSetFree(subject_id);
+        }
+
+	first_time = FALSE;
+	last_seqalign = seqalign_var;
+	seqalign_var = seqalign_var->next;
+    }
+    
+    /* count number of good and bad alignments */
+    for (gsl = GoodSeqAlignments, countGood = 0; gsl; gsl = gsl->next, 
+             countGood++);
+    for (gsl = BadSeqAlignments, countBad = 0; gsl; gsl = gsl->next, 
+             countBad++);
+    
+    if (countGood + countBad)
+	/* allocate memo for marks array */
+	marks = (Int2Ptr) MemNew(sizeof(Int2) * (countGood + countBad));
+    else
+	marks = NULL;
+    
+    *GoodSeqAlignment_ptr = GoodSeqAlignments;
+    *BadSeqAlignment_ptr = BadSeqAlignments;
+    *lastGood_ptr = lastGood;
+    *marks_ptr = marks;
+    *countBad_ptr = countBad;
+    *countGood_ptr = countGood;
+    
+    return TRUE;
+}
+
+Boolean TestSTDOut(void)
+{
+    if(write(1, "", 0) < 0) {
+	return FALSE;
+    }
+    return TRUE;
+}
+
+static int LIBCALLBACK WWWTickCallback(Int4 sequence_number, 
+                                       Int4 number_of_positive_hits)
+{
+    if(!TestSTDOut()) {
+	return -1;
+    }
+    
+    /*    fprintf(stdout, "."); */
+
+    printf("<!-- Progress msg from the server %d %d-->\n", 
+           sequence_number, number_of_positive_hits);
+
+    fflush(stdout);
+    
+    return 1;
+}
+
+static void PrintRequestHeader(WWWBlastInfoPtr theInfo)
+{
+    printf("<HTML>\n");
+    printf("<HEAD>\n");
+    printf("<TITLE>BLAST Search Results </TITLE>\n");
+    printf("</HEAD>\n");
+    printf("<BODY BGCOLOR=\"#FFFFFF\" LINK=\"#0000FF\" "
+           "VLINK=\"#660099\" ALINK=\"#660099\">\n");
+    fprintf(stdout, "<map name=img_map1>\n");
+    fprintf(stdout, "<area shape=rect coords=2,1,48,21 "
+            "href=\"http://www.ncbi.nlm.nih.gov\">\n");
+    fprintf(stdout, "<area shape=rect coords=385,1,435,21 "
+            "href=\"%s/blast/index.html\">\n", theInfo->www_root_path);
+    fprintf(stdout, "<area shape=rect coords=436,1,486,21 "
+            "href=\"http://www.ncbi.nlm.nih.gov/Entrez/\">\n");
+    fprintf(stdout, "<area shape=rect coords=487,1,508,21 "
+            "href=\"%s/blast/docs/blast_help.html\">\n", theInfo->www_root_path);
+    fprintf(stdout, "</map>\n"); 
+    fprintf(stdout, "<IMG USEMAP=#img_map1 WIDTH=509 HEIGHT=22 "
+            "SRC=\"%s/blast/images/psi_blast.gif\" ISMAP> \n", 
+            theInfo->www_root_path);
+    printf("<BR><BR><PRE>\n");
+   
+    init_buff_ex(90);
+
+    BlastPrintVersionInfo(theInfo->program, TRUE, stdout);
+    fprintf(stdout, "\n");
+   
+    if (WWWGetValueByName(theInfo->info, "NO_REFERENCE") == NULL) { 
+       if (theInfo->is_phi_blast) {
+          BlastPrintPhiReference(TRUE, 90, stdout);
+       } else {
+          BlastPrintReference(TRUE, 90, stdout);
+       }
+    }
+ 
+    fprintf(stdout, "\n");
+
+    AcknowledgeBlastQuery(theInfo->query_bsp, 70, 
+                          stdout, theInfo->believe_query, TRUE);
+    
+    /*
+       dbinfo = GetDbInfoFromReadDb(search_data->database, 
+       !search_data->db_is_na);
+       PrintDbInformation(dbinfo, 70, search_data->outfp, 
+       search_data->html);
+     */
+
+    PrintDbInformation(theInfo->database, !theInfo->db_is_na, 70, 
+                       stdout, TRUE);
+    free_buff();
+
+    fprintf(stdout, "Searching please wait...");
+    
+    fflush(stdout);
+    
+    return;
+}
+
+static ValNodePtr seed_core_private (BlastSearchBlkPtr search, CharPtr program_name, BLAST_OptionsBlkPtr options, SeqLocPtr *seqloc_ptr, CharPtr patfile, CharPtr pattern, Uint1Ptr query, Uint1Ptr unfilter_query, Int4 queryLength, Boolean show_diagnostics, Nlm_FloatHi *paramC, ValNodePtr PNTR info_vnp)
+     
+{
+    Boolean tmp_file_made = FALSE;
+    Char buffer[PATH_MAX];
+    posSearchItems *posSearch;
+    SeqLocPtr seqloc;
+
+    FILE *patfp; 
+    seedSearchItems *seedSearch;
+    Int4 program_flag;
+    Boolean is_dna = FALSE; /*cannot use DNA queries in blastpgp*/
+    Int4 i; /*index over characters*/
+    ValNodePtr vnp;
+    
+    
+    if (search == NULL)
+        return NULL;
+    
+    program_flag = convertProgramToFlag(program_name, &is_dna);
+    
+    if (options->isPatternSearch) {
+        if (pattern) {
+            /* open and fill a temporary file if there's a pattern. XXX */
+            TmpNam(buffer);
+            patfp = FileOpen(buffer, "w");
+            fprintf(patfp, "ID \n");
+            fprintf(patfp, "PA   %s\n", pattern);
+            fflush(patfp);
+            FileClose(patfp);
+            patfp = NULL;
+            tmp_file_made = TRUE;
+        }
+
+        if (patfile)	/* If a file was give, use it. */
+            StringCpy(buffer, patfile);
+        if ((patfp = FileOpen(buffer, "r")) == NULL) {
+            ErrPostEx(SEV_FATAL, 0, 0, "blast: Unable to open pattern file %s\n", buffer);
+            return NULL;
+        }
+        seedSearch = (seedSearchItems *) MemNew(sizeof(seedSearchItems));
+        fillCandLambda(seedSearch, options->matrix, options);
+    } else {
+        ErrPostEx(SEV_FATAL, 0, 0, "Must be a pattern search");
+        return NULL;
+    }
+    
+    if (paramC)
+        *paramC = seedSearch->paramC;
+    
+    search->gap_align = GapAlignBlkNew(1,1);
+    search->gap_align->gap_open = options->gap_open;
+    search->gap_align->gap_extend = options->gap_extend;
+    search->gap_align->decline_align = (-(BLAST_SCORE_MIN));
+    search->gap_align->x_parameter = options->gap_x_dropoff
+        *NCBIMATH_LN2/seedSearch->paramLambda;
+    search->gap_align->matrix = search->sbp->matrix;
+    initProbs(seedSearch);
+    init_order(search->gap_align->matrix,program_flag,is_dna,seedSearch);
+
+    for(i = 0; i < queryLength; i++)
+        query[i] = seedSearch->order[query[i]];
+    if (unfilter_query) {
+        for(i = 0; i < queryLength; i++)
+            unfilter_query[i] = seedSearch->order[unfilter_query[i]];
+    }
+    
+    seqloc = NULL;
+    posSearch = (posSearchItems *) MemNew(sizeof(posSearchItems));
+    
+    vnp = seedEngineCore(search, options, query, unfilter_query, readdb_get_filename(search->rdfp), patfile, program_flag, patfp, is_dna, FALSE, seedSearch, options->ethresh, 0.0, posSearch, &seqloc, show_diagnostics, info_vnp);
+    
+    if (tmp_file_made)	/* Remove temporary pattern file if it exists. */
+        FileRemove(buffer);
+    
+    MemFree(seedSearch);
+
+    MemFree(posSearch->posResultSequences);
+    MemFree(posSearch);
+
+    *seqloc_ptr = seqloc;
+    
+    return vnp;
+}
+
+static  BLAST_ScorePtr PNTR GetPSIMatrix(PSIDataPtr psidata, WWWBlastInfoPtr theInfo, Nlm_FloatHi *karlinK_out, Nlm_FloatHi ***posFreqs_out) {
+    
+    CharPtr     chptr, Matrix62_last=NULL, pattern;
+    Int4        i;
+    Nlm_FloatHi karlinK;
+    Int2        num_entries;
+    Int4 queryLength; /*length of query sequence*/
+    Int4 numSeqAligns;
+    SeqAlignPtr	seqalign;
+    SeqAlignPtr *lastSeqAligns=NULL;
+    SeqLocPtr seg_slp; /*pointer to structure for seg filtering*/
+    Uint1Ptr query = NULL; /*query sequence read in*/
+    Uint1Ptr unfilter_query = NULL; /*needed if seg will filter query*/
+    ValNodePtr info_vnp, phi_vnp = NULL;
+    SeqLocPtr phi_seqloc = NULL;
+    Uint4      gi;
+    SeqIdPtr   sip, all_sip = NULL;
+
+    BlastSearchBlkPtr search;
+    BLAST_ScorePtr PNTR posMatrix = NULL;
+    compactSearchItems *compactSearch = NULL;
+    CharPtr CHARPosFreqs_last;
+    Nlm_FloatHi **posFreqs;
+
+    /* first step; return NULL, means to use default matrix */
+    if (psidata->StepNumber == 0) 
+	return NULL;
+        
+    /* The second step;  means, that there is list of GI's to 
+       recalculate matrix 
+       using default or read matrix and list of seqaligns 
+       from limited search;  limited search -
+       search the query not in whole database but just
+       in subset specified byt the list of GI's
+     */
+
+    /* Create list of SeqIdPtr for the limited search */
+
+    num_entries = WWWGetNumEntries(theInfo->info);
+
+    for(i = 0; i < num_entries; i++) {
+	GIListPtr	good_gil, checked_gil;
+        
+	if((chptr = WWWGetNameByIndex(theInfo->info, i)) != NULL && 
+           !StringICmp(chptr, "checked_GI")) {
+            
+	    if((chptr = WWWGetValueByIndex(theInfo->info, i)) != NULL) {
+                gi = atoi(chptr);                
+		sip = ValNodeAddInt(NULL, SEQID_GI, gi);
+                ValNodeLink(&all_sip, sip);
+
+		/* Create list of GI's, it will be used when we
+		   test convergence */
+                
+		if (!psidata->PrevCheckedGIs) {
+		    /* first one */
+		    checked_gil = (GIListPtr) MemNew(sizeof(GIList));
+		    checked_gil->gi = gi;
+		    checked_gil->next = NULL;
+		    psidata->PrevCheckedGIs = checked_gil;
+		} else {
+		    checked_gil->next = (GIListPtr) MemNew(sizeof(GIList));
+		    checked_gil = checked_gil->next;
+		    checked_gil->gi = gi;
+		    checked_gil->next = NULL;
+		}
+	    }
+	} else if((chptr = WWWGetNameByIndex(theInfo->info, i)) != NULL && 
+                  !StringICmp(chptr, "good_GI")) {
+            
+	    if((chptr = WWWGetValueByIndex(theInfo->info, i)) != NULL) {
+                gi = atoi(chptr);
+                
+		if (!psidata->PrevGoodGIs) {
+		    /* first one */
+		    good_gil = (GIListPtr) MemNew(sizeof(GIList));
+		    good_gil->gi = gi;
+		    good_gil->next = NULL;
+		    psidata->PrevGoodGIs = good_gil;
+		} else {
+		    good_gil->next = (GIListPtr) MemNew(sizeof(GIList));
+		    good_gil = good_gil->next;
+		    good_gil->gi = gi;
+		    good_gil->next = NULL;
+		}
+	    }
+	}
+    }
+
+    /* So this search will be limited to the list of gis */
+    theInfo->options->gilist = all_sip;
+    
+    /* Some additional parameters required for the matrix recalculation */
+    
+    theInfo->options->use_best_align = TRUE;
+    theInfo->options->use_real_db_size = TRUE;
+    
+    /* the search */
+
+    if((search = BLASTSetUpSearchWithReadDb(theInfo->fake_bsp, theInfo->program, theInfo->query_bsp->length, theInfo->database, theInfo->options, WWWTickCallback ))  == NULL) {
+	return NULL;
+    } 
+    
+    search->positionBased = FALSE;
+    
+    if (psidata->StepNumber > 1) {
+	/* The third and rest of steps;  means, that
+	   before we are recalculating matrix, we 
+	   should read old matrix from the previous step;
+        */
+        
+	/* Read matrix from the previous step */
+        
+        Matrix62_last = WWWGetValueByName(theInfo->info, "PSI_MATRIX");
+        
+	/* Decode read matrix */
+        
+	if(Matrix62_last != NULL && Matrix62_last[0] != NULLB) {
+	    search->positionBased = TRUE;
+	    search->sbp->posMatrix = Decode62Matrix (Matrix62_last, search->context[0].query->length, search->sbp->alphabet_size);
+	}
+        
+        CHARPosFreqs_last = WWWGetValueByName(theInfo->info, "POS_FREQS");
+        
+        if(CHARPosFreqs_last != NULL && CHARPosFreqs_last[0] != NULLB) {
+	    search->positionBased = TRUE;
+            search->sbp->posFreqs = BLASTDecodePosFreqs(CHARPosFreqs_last, search->context[0].query->length, search->sbp->alphabet_size);
+
+#if 0
+        {{
+            FILE *fd;
+            fd = FileOpen("/tmp/new_freqs.float", "w");
+            for(i = 0; i <= search->context[0].query->length; i++) {
+                for(j =0; j < search->sbp->alphabet_size; j++) {        
+                    fprintf(fd, "%f ", search->sbp->posFreqs[i][j]);
+                }
+                fprintf(fd, "\n");
+            }
+        }}
+#endif
+
+
+        }
+        
+        if((chptr = WWWGetValueByName(theInfo->info, 
+                                      "PSI_KARLIN_K")) != NULL) {
+            karlinK = atof(chptr);
+            search->sbp->kbp_gap_psi[0]->K = karlinK;
+            search->sbp->kbp_gap_psi[0]->logK = log(karlinK);
+        }
+	
+    } /* end reread the matrix */    
+
+    search->thr_info->tick_callback = NULL;
+    
+    pattern = WWWGetValueByName(theInfo->info, "PHI_PATTERN");
+    
+    /* If pattern is non-NULL, then it is a PHI-BLAST search. */
+    if (pattern) {
+        query = BlastGetSequenceFromBioseq(theInfo->fake_bsp, &queryLength);
+        seg_slp = BlastBioseqFilter(theInfo->fake_bsp, theInfo->options->filter_string);
+        unfilter_query = NULL;
+        if (seg_slp) {
+            unfilter_query = MemNew((queryLength + 1) * sizeof(Uint1));
+            for (i = 0; i < queryLength; i++)
+                unfilter_query[i] = query[i];
+            BlastMaskTheResidues(query,queryLength,21,seg_slp,FALSE, 0);
+        }
+        
+	theInfo->options->isPatternSearch = TRUE;
+	phi_vnp = seed_core_private(search, "patseedp", theInfo->options, &phi_seqloc, NULL, pattern, query, unfilter_query, queryLength, FALSE, NULL, &info_vnp);
+        ValNodeFreeData(info_vnp);
+
+        MemFree(query);
+        MemFree(unfilter_query);
+        
+	seqalign = convertValNodeListToSeqAlignList(phi_vnp, &lastSeqAligns, &numSeqAligns);
+        ValNodeFree(phi_vnp);
+    } else {
+    	seqalign = BioseqBlastEngineCore(search, theInfo->options, 
+                                         search->sbp->posMatrix);
+    }
+    
+    if(search->sbp->posMatrix != NULL) {
+        for(i = 0; i <= theInfo->fake_bsp->length; i++) {
+            MemFree(search->sbp->posMatrix[i]);
+        }    
+        MemFree(search->sbp->posMatrix);
+        search->sbp->posMatrix = NULL;
+    }
+
+    /* Now finaly calculating matrix that will be used at this step */
+    
+    if(seqalign) {
+
+        ReadDBBioseqFetchEnable("psiblast", theInfo->database, 
+                                FALSE, TRUE);
+        compactSearch = compactSearchNew(compactSearch);
+        copySearchItems(compactSearch, search, theInfo->options->matrix);
+
+        compactSearch->pseudoCountConst = 7;
+
+        if (search->sbp->posFreqs == NULL) {
+            search->sbp->posFreqs =  allocatePosFreqs(compactSearch->qlength, 
+                                                      compactSearch->alphabetSize);
+        }
+        
+        posMatrix = WposComputation(compactSearch, seqalign, 
+                                    search->sbp->posFreqs);
+
+        /* We have to return posFreqs to the upper layer */
+        posFreqs =  allocatePosFreqs(compactSearch->qlength, 
+                                     compactSearch->alphabetSize);
+        copyPosFreqs(search->sbp->posFreqs, posFreqs, compactSearch->qlength, 
+                     compactSearch->alphabetSize);
+
+        MemFree(compactSearch->standardProb);
+        MemFree(compactSearch);
+
+        ReadDBBioseqFetchDisable();
+        
+	/* Encode matrix for the use in the next step*/
+        
+	psidata->matrix62 = Encode62Matrix(posMatrix, 
+                                           search->context[0].query->length, 
+                                           search->sbp->alphabet_size);
+
+        psidata->CHARPosFreqs = BLASTEncodePosFreqs(posFreqs, search->context[0].query->length, search->sbp->alphabet_size);
+
+#if 0
+        {{
+            FILE *fd;
+            fd = FileOpen("/tmp/old_freqs.float", "w");
+            for(i = 0; i <= search->context[0].query->length; i++) {
+                for(j =0; j < search->sbp->alphabet_size; j++) {        
+                    fprintf(fd, "%f ", posFreqs[i][j]);
+                }
+                fprintf(fd, "\n");
+            }
+            FileClose(fd);
+            fd = FileOpen("/tmp/old_freqs.buffer", "w");
+            fprintf(fd, "%s", psidata->CHARPosFreqs);
+            FileClose(fd);            
+        }}
+#endif
+    }
+    
+    *karlinK_out = search->sbp->kbp_gap_psi[0]->K;
+    *posFreqs_out = posFreqs;
+
+    SeqAlignSetFree(seqalign);
+    SeqLocFree(phi_seqloc);
+    
+    search = BlastSearchBlkDestruct(search);
+
+    theInfo->options->use_best_align = FALSE;
+    theInfo->options->use_real_db_size = FALSE;
+
+    SeqIdSetFree(theInfo->options->gilist);
+    theInfo->options->gilist = NULL;
+    theInfo->options->isPatternSearch = FALSE;
+    
+    return posMatrix;
+} /* end of GetPSIMatrix() */
+
+BLASTPrintDataPtr PSIBlastSearch(WWWBlastInfoPtr theInfo)
+{
+    BLASTPrintDataPtr print_data;
+    ValNodePtr vnp, other_returns= NULL;
+    Int4 i;
+    PSIDataPtr psidata;
+    CharPtr    chptr;
+    BlastSearchBlkPtr search;
+    BLAST_ScorePtr PNTR posMatrix = NULL;
+    Nlm_FloatHi karlinK;
+    Nlm_FloatHi **posFreqs;
+    
+    if(theInfo == NULL)
+	return NULL;
+
+    PrintRequestHeader(theInfo); 
+    print_data = (BLASTPrintDataPtr) MemNew(sizeof(BLASTPrintData));
+    
+    psidata = MemNew(sizeof(PSIData));
+    psidata->PrevGoodGIs = NULL;
+    psidata->PrevCheckedGIs = NULL;
+    
+    /* initialize the search */
+    theInfo->options->pseudoCountConst = 7;
+
+    if((search = BLASTSetUpSearchWithReadDb(theInfo->fake_bsp, theInfo->program, theInfo->query_bsp->length, theInfo->database, theInfo->options, WWWTickCallback ))  == NULL) {
+	return NULL;
+    }
+
+    /* Matrix and StepNumber for PSI-Blast */
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "STEP_NUMBER")) != NULL)
+	psidata->StepNumber = atoi(chptr);
+    
+    if((posMatrix = GetPSIMatrix(psidata, theInfo, 
+                                 &karlinK, &posFreqs)) != NULL) {
+        search->positionBased = TRUE;
+        search->sbp->kbp_gap_psi[0]->K = karlinK;
+        search->sbp->kbp_gap_psi[0]->logK = log(karlinK);
+        search->sbp->posFreqs = posFreqs;
+    }
+    
+    search->sbp->posMatrix = posMatrix;
+    
+    search->thr_info->tick_callback = WWWTickCallback;
+
+    ReadDBBioseqFetchEnable("psiblast", theInfo->database, 
+                            FALSE, TRUE);    
+    printf("</PRE>\n");
+    print_data->seqalign = BioseqBlastEngineCore(search, theInfo->options, posMatrix);
+
+    ReadDBBioseqFetchDisable();
+
+#if 0
+    if(seqalign) {
+
+        ReadDBBioseqFetchEnable("psiblast", theInfo->database, 
+                                FALSE, TRUE);
+        compactSearch = compactSearchNew(compactSearch);
+        copySearchItems(compactSearch, search, theInfo->options->matrix);
+
+        compactSearch->pseudoCountConst = 7;
+
+        if (search->sbp->posFreqs == NULL) {
+            search->sbp->posFreqs =  allocatePosFreqs(compactSearch->qlength, 
+                                                      compactSearch->alphabetSize);
+        }
+        
+        posMatrix = WposComputation(compactSearch, seqalign, 
+                                    search->sbp->posFreqs);
+
+        MemFree(compactSearch->standardProb);
+        MemFree(compactSearch);
+
+        
+	/* Encode matrix for the use in the next step*/
+    }
+#endif
+
+    if(posMatrix != NULL) {
+        for(i = 0; i <= theInfo->fake_bsp->length; i++) {
+            MemFree(posMatrix[i]);
+        }
+        
+        MemFree(posMatrix);
+        search->sbp->posMatrix = NULL;
+    }
+
+    print_data->psidata = psidata;
+    
+    /*  Blast search */
+    
+    other_returns = BlastOtherReturnsPrepare(search);
+
+    print_data->mask_loc = NULL;
+
+    for (vnp=other_returns; vnp; vnp = vnp->next) {
+	switch (vnp->choice) {
+        case TXDBINFO:
+            print_data->dbinfo = vnp->data.ptrvalue;
+            break;
+        case TXKABLK_NOGAP:
+            print_data->ka_params = 
+                (BLAST_KarlinBlkPtr) vnp->data.ptrvalue;
+            break;
+        case TXKABLK_GAP:
+            print_data->ka_params_gap = 
+                (BLAST_KarlinBlkPtr) vnp->data.ptrvalue;
+            psidata->karlinK = print_data->ka_params_gap->K;
+            break;
+        case TXPARAMETERS:
+            print_data->buffer = vnp->data.ptrvalue;
+            break;
+        case TXMATRIX:
+            print_data->matrix = (BLAST_MatrixPtr) vnp->data.ptrvalue;
+            /*BLAST_MatrixDestruct(matrix);*/
+            vnp->data.ptrvalue = NULL;
+            break;
+        case SEQLOC_MASKING_NOTSET:
+        case SEQLOC_MASKING_PLUS1:
+        case SEQLOC_MASKING_PLUS2:
+        case SEQLOC_MASKING_PLUS3:
+        case SEQLOC_MASKING_MINUS1:
+        case SEQLOC_MASKING_MINUS2:
+        case SEQLOC_MASKING_MINUS3:
+            ValNodeAddPointer(&(print_data->mask_loc), vnp->choice, vnp->data.ptrvalue);
+            break;
+        default:
+            break;
+	}
+    }   
+
+    ValNodeFree(other_returns);
+
+    search = BlastSearchBlkDestruct(search);
+
+    return print_data;
+}
+
+BLASTPrintDataPtr PHIBlastSearch(WWWBlastInfoPtr theInfo)
+{
+    BLASTPrintDataPtr print_data;
+    ValNodePtr vnp, other_returns= NULL;
+    PSIDataPtr psidata;
+    Nlm_FloatHi paramC;
+    Int4 i;
+    Int4 queryLength; /*length of query sequence*/
+    CharPtr chptr;
+    Char	matrixname[64] = "BLOSUM62";
+    Int4	opencost = 0, extendedcost = 0;
+    SeqLocPtr seg_slp; /*pointer to structure for seg filtering*/
+    Uint1Ptr query = NULL; /*query sequence read in*/
+    Uint1Ptr unfilter_query = NULL; /*needed if seg will filter query*/
+    ValNodePtr info_vnp;
+    BlastSearchBlkPtr search;
+
+    if(theInfo == NULL)
+	return NULL;
+    
+    PrintRequestHeader(theInfo); 
+    print_data = (BLASTPrintDataPtr) MemNew(sizeof(BLASTPrintData));
+    
+    psidata = MemNew(sizeof(PSIData));
+    psidata->PrevGoodGIs = NULL;
+    psidata->PrevCheckedGIs = NULL;
+    
+    print_data->psidata = psidata;
+    
+    /* Get matrix name and gap costs */
+    
+    if((chptr = WWWGetValueByName(theInfo->info, "MAT_PARAM")) != NULL) {
+	if (chptr[1] != '-' || chptr[2] != '-')
+	    sscanf(chptr, "%s\t %d\t %d", matrixname, &opencost, &extendedcost);
+    }
+
+    /* Change matrix parameters */
+    
+    BLASTOptionSetGapParams (theInfo->options, matrixname, 
+                             opencost, extendedcost);
+    
+    chptr = WWWGetValueByName(theInfo->info, "PHI_PATTERN");
+    
+    /* Reguilar PHI-Blast search */
+    theInfo->options->isPatternSearch = TRUE;
+    
+    if((search = BLASTSetUpSearchWithReadDb(theInfo->fake_bsp, "blastp", theInfo->query_bsp->length, theInfo->database, theInfo->options, WWWTickCallback))  == NULL) {
+	return NULL;
+    }
+    
+    query = BlastGetSequenceFromBioseq(theInfo->fake_bsp, &queryLength);
+    seg_slp = BlastBioseqFilter(theInfo->fake_bsp, 
+                                theInfo->options->filter_string);
+    
+    unfilter_query = NULL;
+    if (seg_slp) {
+        unfilter_query = MemNew((queryLength + 1) * sizeof(Uint1));
+        for (i = 0; i < queryLength; i++)
+            unfilter_query[i] = query[i];
+        BlastMaskTheResidues(query,queryLength,21,seg_slp,FALSE, 0);
+    }
+    
+    print_data->vnp = seed_core_private(search, "patseedp", theInfo->options, &(print_data->seqloc), NULL, chptr, query, unfilter_query, queryLength, TRUE, &paramC, &info_vnp);
+    
+    print_data->info_vnp = info_vnp;
+    
+    MemFree(query);
+    MemFree(unfilter_query);
+    
+    /*  Blast search */
+    
+    other_returns = BlastOtherReturnsPrepare(search);
+    print_data->mask_loc = NULL;
+    for (vnp=other_returns; vnp; vnp = vnp->next) {
+	switch (vnp->choice) {
+        case TXDBINFO:
+            print_data->dbinfo = vnp->data.ptrvalue;
+            break;
+        case TXKABLK_GAP:
+            print_data->ka_params_gap = vnp->data.ptrvalue;
+            /* print_data->ka_params_gap->paramC = paramC; ?? */
+            break;
+        case TXKABLK_NOGAP:
+            print_data->ka_params = vnp->data.ptrvalue;
+            break;
+        case TXPARAMETERS:
+            print_data->buffer = vnp->data.ptrvalue;
+            break;
+        case TXMATRIX:
+            print_data->matrix = (BLAST_MatrixPtr) vnp->data.ptrvalue;
+            /*BLAST_MatrixDestruct(matrix);*/
+            vnp->data.ptrvalue = NULL;
+            break;
+        case SEQLOC_MASKING_NOTSET:
+        case SEQLOC_MASKING_PLUS1:
+        case SEQLOC_MASKING_PLUS2:
+        case SEQLOC_MASKING_PLUS3:
+        case SEQLOC_MASKING_MINUS1:
+        case SEQLOC_MASKING_MINUS2:
+        case SEQLOC_MASKING_MINUS3:
+            ValNodeAddPointer(&(print_data->mask_loc), vnp->choice, vnp->data.ptrvalue);
+            break;
+        default:
+            break;
+        }
+    }
+    
+    search = BlastSearchBlkDestruct(search);
+    
+    fflush(stdout);
+    return print_data;
+}
+
+static	void	printSubmitButton(FILE* fp, Int4 step)
+{
+    fprintf(fp, "<INPUT TYPE=\"submit\" NAME=\"NEXT_I\" "
+            "VALUE=\"Run PSI-Blast iteration %d\">\n", 
+            step);
+}
+
+static Int4 get_number_alignment(SeqAlignPtr align)
+{
+    Int4 num = 0;
+    
+    while(align) {
+	++num;
+	align = align->next;
+    }
+    
+    return num;
+}
+
+Boolean PHIPrintOutput(WWWBlastInfoPtr theInfo,
+	BLASTPrintDataPtr print_data, 
+	ValNodePtr vnp, Nlm_FloatHi ethresh_old)
+{
+    Uint4 align_options, print_options;
+    SeqAnnotPtr seqannot;
+    BlastTimeKeeper time_keeper;
+    Uint1 f_order[FEATDEF_ANY], g_order[FEATDEF_ANY];
+    Char	href[1024];
+    Char	f_name[64], title[1024];
+    Int4	align_num;
+    Int2	countBad, countGood;
+    Int2Ptr 	marks;
+    Int4 numSeqAligns;
+    SeqAlignPtr	seqalign;
+    SeqAlignPtr *lastSeqAligns=NULL;
+    SeqAlignPtr	lastGood, BadSeqAlignments, GoodSeqAlignments;
+    SeqLocPtr	seqloc;
+    ValNodePtr	vnp_var;
+    Int4Ptr PNTR txmatrix;
+
+    MemSet((Pointer)(g_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
+    MemSet((Pointer)(f_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
+    
+    if(print_data == NULL) {
+        WWWBlastErrMessage(BLASTMiscError, NULL);                
+	return FALSE;
+    }
+
+    print_options = 0;
+    align_options = 0;
+
+    align_options += TXALIGN_COMPRESS;
+    align_options += TXALIGN_END_NUM;
+
+    if (theInfo->show_gi) {
+	align_options += TXALIGN_SHOW_GI;
+	print_options += TXALIGN_SHOW_GI;
+    }
+
+    if (theInfo->options->gapped_calculation == FALSE)
+	print_options += TXALIGN_SHOW_NO_OF_SEGS;
+
+
+    if (theInfo->align_view != Pairwise) {
+        align_options += TXALIGN_MASTER;
+        if (theInfo->align_view == QueryAnchoredIdent || 
+            theInfo->align_view == FlatQueryAnchoredIdent)
+            align_options += TXALIGN_MISMATCH;
+        if (theInfo->align_view == FlatQueryAnchoredIdent || 
+            theInfo->align_view == FlatQueryAnchoredNoIdent || 
+            theInfo->align_view == FlatQueryAnchoredBluntEnd)
+            align_options += TXALIGN_FLAT_INS;
+        if (theInfo->align_view == QueryAnchoredBluntEnd || 
+            theInfo->align_view == FlatQueryAnchoredBluntEnd)
+            align_options += TXALIGN_BLUNT_END;
+    } else {
+	align_options += TXALIGN_MATRIX_VAL;
+	align_options += TXALIGN_SHOW_QS;
+    }
+
+    /* align_options += TXALIGN_MATRIX_VAL;
+       align_options += TXALIGN_SHOW_QS; */
+
+    align_options += TXALIGN_HTML;
+    print_options += TXALIGN_HTML; 
+
+    ReadDBBioseqFetchEnable ("phiblast", 
+                             theInfo->database,  theInfo->db_is_na, TRUE);
+    
+    seqannot = SeqAnnotNew();
+    seqannot->type = 2;
+    AddAlignInfoToSeqAnnot(seqannot, theInfo->align_type);
+
+    init_buff();
+
+    /*    gethostname(hostname, sizeof(hostname)); */
+
+    sprintf(href, "nph-viewgif.cgi?");
+    
+    seqalign = convertValNodeListToSeqAlignList(print_data->vnp, &lastSeqAligns, &numSeqAligns);
+    seqannot->data = seqalign;
+    if (theInfo->show_overview) {
+        sprintf(f_name, "%ld%ld.gif", (long)random(), (long)getpid());
+        align_num = get_number_alignment((SeqAlignPtr)(seqannot->data)); 
+        sprintf(title, "<H3><a href=\"%s/blast/docs/newoptions.html#graphical-overview\"> "
+                "Distribution of %ld Blast Hits on the Query Sequence</a></H3>\n", theInfo->www_root_path, (long)align_num);  
+        
+        PrintAlignmentOverview(seqannot, stdout, "PSI_BLAST", href, f_name, title); 
+    }
+
+    seqannot->data = NULL;
+    seqannot = SeqAnnotFree(seqannot);
+    
+    print_data->vnp = convertSeqAlignListToValNodeList(seqalign, lastSeqAligns, numSeqAligns);
+    
+    print_options += TXALIGN_DO_NOT_PRINT_TITLE; 
+    print_options += TXALIGN_CHECK_BOX;
+    if (print_data->psidata->StepNumber)
+        print_options += TXALIGN_NEW_GIF;
+    
+    /* submit button */
+    printSubmitButton(stdout, 
+                      print_data->psidata->StepNumber+1);
+    
+    if (print_data->psidata->StepNumber && theInfo->number_of_descriptions) {
+        printf("<HR><p><b>Legend:</b><p>\
+<IMG SRC=\"%s/blast/images/new.gif\" WIDTH=25 HEIGHT=15> - means that \
+the alignment score was below the threshold on the previous iteration \
+<p>\
+<IMG SRC=\"%s/blast/images/checked.gif\" WIDTH=15 HEIGHT=15> - means that \
+the alignment was checked on the previous iteration \
+</p>", theInfo->www_root_path, theInfo->www_root_path);
+    }
+    
+    /*
+      if (theInfo->number_of_descriptions) {
+      if (print_data->psidata->StepNumber)
+      printf("\n<IMG SRC=\"/BLAST/bg.gif\" WIDTH=65 HEIGHT=15>");
+      printf("                                                                     Score    E");
+      printf("\nSequences producing significant alignments:");
+      if (print_data->psidata->StepNumber)
+      printf("<IMG SRC=\"/BLAST/bg.gif\" WIDTH=65 HEIGHT=15>");
+      printf("                          (bits) Value\n\n");
+      }
+    */
+    
+    vnp_var = vnp;
+    seqloc = print_data->seqloc;
+    marks = NULL;
+    while (vnp_var) {
+        SplitSeqAlign((SeqAlignPtr) vnp_var->data.ptrvalue, &GoodSeqAlignments, &BadSeqAlignments, &lastGood, &marks, 
+                      &countBad, &countGood, ethresh_old);
+	
+        printf("<HR><CENTER><b><FONT color=\"green\">"
+               "Sequences with pattern at position %d and E-value BETTER than threshold</FONT></b></CENTER>\n",
+               SeqLocStart(seqloc)+1);
+        
+        if (print_data->psidata->StepNumber)
+            printf("\n<IMG SRC=\"%s/blast/images/bg.gif\" WIDTH=65 HEIGHT=15>", 
+                   theInfo->www_root_path);
+        printf("                                                                     Score    E");
+        printf("\nSequences producing significant alignments:");
+        if (print_data->psidata->StepNumber)
+            printf("<IMG SRC=\"%s/blast/images/bg.gif\" WIDTH=65 HEIGHT=15>",
+                   theInfo->www_root_path);
+        printf("                          (bits) Value\n\n");
+        
+        fflush(stdout);
+        print_options += TXALIGN_CHECK_BOX_CHECKED;
+        PrintDefLinesFromSeqAlignEx(GoodSeqAlignments, 80, stdout, print_options, FIRST_PASS, marks, theInfo->number_of_descriptions);
+        
+        print_options -= TXALIGN_CHECK_BOX_CHECKED;
+        
+        if (print_data->psidata->StepNumber == 0)
+            printf("<a name = Evalue> </a>");
+	
+        if (theInfo->number_of_descriptions > countGood && BadSeqAlignments) {
+            /* submit button */
+            printSubmitButton(stdout, print_data->psidata->StepNumber+1);
+            
+            printf("<HR><CENTER><b><FONT color=\"green\">"
+                   "Sequences with pattern at position %d and E-value WORSE than threshold</FONT></b></CENTER>\n", 
+                   SeqLocStart(seqloc)+1);
+            
+            PrintDefLinesFromSeqAlignEx(BadSeqAlignments, 80, stdout, print_options, FIRST_PASS, &marks[countGood], theInfo->number_of_descriptions - countGood);
+        }
+
+        marks = MemFree(marks);
+        
+        /* merge lists */
+        if (lastGood)
+            lastGood->next = BadSeqAlignments;
+        
+        vnp_var = vnp_var->next;
+        seqloc = seqloc->next;
+    }
+    
+    if (theInfo->number_of_descriptions) {
+        /* submit button */
+        printSubmitButton(stdout, 
+                          print_data->psidata->StepNumber+1);
+    }
+    
+    free_buff();
+    fflush(stdout);
+
+    fprintf(stdout, "<HR>");
+
+    txmatrix = NULL;
+    if (print_data->matrix)
+       txmatrix = (Int4Ptr PNTR) BlastMatrixToTxMatrix(print_data->matrix);
+
+    if (theInfo->number_of_alignments) {
+	fprintf(stdout, "<CENTER><b><FONT color=\"green\">"
+		"Alignments</FONT></b></CENTER>\n");
+        
+        f_order[FEATDEF_REGION] = 1;
+        g_order[FEATDEF_REGION] = 1;
+        if(theInfo->align_view == Pairwise) {
+            ShowTextAlignFromAnnotExtra(theInfo->fake_bsp, 
+                                        print_data->vnp, 
+                                        print_data->seqloc, 60, 
+                                        stdout, 
+                                        f_order, g_order, align_options, 
+                                        txmatrix, print_data->mask_loc, 
+                                        FormatScoreFunc);
+        } else {
+            ShowTextAlignFromAnnotExtra(theInfo->fake_bsp, 
+                                        print_data->vnp, 
+                                        print_data->seqloc, 60, 
+                                        stdout, 
+                                        f_order, g_order, align_options, 
+                                        txmatrix, print_data->mask_loc, 
+                                        NULL);
+            printf("<P>\n");
+        }
+    }
+
+    fflush(stdout);
+    ObjMgrClearHold(); 
+
+    printf("<PRE>\n");
+
+    BlastTimeFillStructure(&time_keeper);
+
+    fprintf(stdout, "CPU time: %8.2f user secs.\t%8.2f sys. "
+	    "secs\t%8.2f total secs.\n\n", 
+	    time_keeper.user, time_keeper.system, time_keeper.total);    
+    
+    if (txmatrix)
+           txmatrix =  (Int4Ptr PNTR) TxMatrixDestruct(txmatrix);
+    print_data->matrix = BLAST_MatrixDestruct(print_data->matrix);
+
+    init_buff();
+    PrintDbReport(print_data->dbinfo, 70, stdout);
+    
+    fflush(stdout);
+    if (print_data->ka_params_gap) {
+        PrintKAParameters(print_data->ka_params_gap->Lambda, 
+                          print_data->ka_params_gap->K, 
+                          print_data->ka_params_gap->H, 
+                          70, stdout, TRUE);
+    }
+    fflush(stdout);
+    
+    PGPOutTextMessages(print_data->info_vnp, stdout);
+
+    PrintTildeSepLines(print_data->buffer, 70, stdout);
+    free_buff();
+
+    fflush(stdout);
+
+    ReadDBBioseqFetchDisable();
+
+    return TRUE;
+}
+
+Boolean PSIPrintOutput(WWWBlastInfoPtr theInfo,
+	BLASTPrintDataPtr print_data, 
+	SeqAlignPtr BadSeqAlignments, SeqAlignPtr GoodSeqAlignments,
+	SeqAlignPtr lastGood,
+	Int2Ptr marks, Int2 countBad, Int2 countGood,
+	Nlm_FloatHi ethresh_old)
+{
+    Uint4 align_options, print_options;
+    SeqAnnotPtr seqannot;
+    BlastTimeKeeper time_keeper;
+    BlastPruneSapStructPtr prune;
+    Uint1 f_order[FEATDEF_ANY], g_order[FEATDEF_ANY];
+    Char	href[1024];
+    Char	f_name[64], title[1024];
+    Int4	align_num;
+    Int4Ptr PNTR txmatrix;
+
+    MemSet((Pointer)(g_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
+    MemSet((Pointer)(f_order), 0, (size_t)(FEATDEF_ANY* sizeof(Uint1)));
+    
+    if(print_data == NULL) {
+        WWWBlastErrMessage(BLASTMiscError, NULL);                
+	return FALSE;
+    }
+    
+    print_options = 0;
+    align_options = 0;
+    
+    align_options += TXALIGN_COMPRESS;
+    align_options += TXALIGN_END_NUM;
+    
+    if (theInfo->show_gi) {
+	align_options += TXALIGN_SHOW_GI;
+	print_options += TXALIGN_SHOW_GI;
+    }
+    
+    if (theInfo->options->gapped_calculation == FALSE)
+	print_options += TXALIGN_SHOW_NO_OF_SEGS;
+    
+    if (theInfo->align_view != Pairwise) {
+        align_options += TXALIGN_MASTER;
+        if (theInfo->align_view == QueryAnchoredIdent || 
+            theInfo->align_view == FlatQueryAnchoredIdent)
+            align_options += TXALIGN_MISMATCH;
+        if (theInfo->align_view == FlatQueryAnchoredIdent || 
+            theInfo->align_view == FlatQueryAnchoredNoIdent || 
+            theInfo->align_view == FlatQueryAnchoredBluntEnd)
+            align_options += TXALIGN_FLAT_INS;
+        if (theInfo->align_view == QueryAnchoredBluntEnd || 
+            theInfo->align_view == FlatQueryAnchoredBluntEnd)
+            align_options += TXALIGN_BLUNT_END;
+    } else {
+	align_options += TXALIGN_MATRIX_VAL;
+	align_options += TXALIGN_SHOW_QS;
+    }
+    
+    /* align_options += TXALIGN_MATRIX_VAL;
+       align_options += TXALIGN_SHOW_QS; */
+
+    align_options += TXALIGN_HTML;
+    print_options += TXALIGN_HTML; 
+
+    ReadDBBioseqFetchEnable ("psiblast", 
+	    theInfo->database, 
+	    theInfo->db_is_na, 
+	    TRUE);
+
+    seqannot = SeqAnnotNew();
+    seqannot->type = 2;
+    AddAlignInfoToSeqAnnot(seqannot, theInfo->align_type);
+    seqannot->data = print_data->seqalign;
+
+    init_buff();
+
+    /* merge lists */
+    if (lastGood)
+        lastGood->next = BadSeqAlignments;
+    
+    /* gethostname(hostname, sizeof(hostname)); */
+    
+    sprintf(href, "nph-viewgif.cgi?");
+    
+    if (theInfo->show_overview) {
+        sprintf(f_name, "%ld%ld.gif", (long)random(), (long)getpid());
+        align_num = get_number_alignment((SeqAlignPtr)(seqannot->data)); 
+        sprintf(title, "<H3><a href=\"%s/blast/docs/newoptions.html#graphical-overview\"> "
+                "Distribution of %ld Blast Hits on the Query Sequence</a></H3>\n", theInfo->www_root_path, (long)align_num);  
+        
+        PrintAlignmentOverview(seqannot, stdout, "PSI_BLAST", href, f_name, title); 
+    }
+    
+    /* separate lists */
+    if (lastGood)
+        lastGood->next = NULL;
+    
+    print_options += TXALIGN_DO_NOT_PRINT_TITLE; 
+    print_options += TXALIGN_CHECK_BOX;
+    print_options += TXALIGN_CHECK_BOX_CHECKED;
+    if (print_data->psidata->StepNumber)
+        print_options += TXALIGN_NEW_GIF;
+    
+    /* submit button */
+    printSubmitButton(stdout, 
+                      print_data->psidata->StepNumber+1);
+    
+    if (print_data->psidata->StepNumber && theInfo->number_of_descriptions) {
+        printf("<HR><p><b>Legend:</b><p>\
+<IMG SRC=\"%s/blast/images/new.gif\" WIDTH=25 HEIGHT=15> - means that \
+the alignment score was below the threshold on the previous iteration \
+<p>\
+<IMG SRC=\"%s/blast/images/checked.gif\" WIDTH=15 HEIGHT=15> - means that \
+the alignment was checked on the previous iteration \
+</p>", theInfo->www_root_path, theInfo->www_root_path);
+    }
+    
+    if (theInfo->number_of_descriptions) {
+        printf("<HR><CENTER><b><FONT color=\"green\">"
+               "Sequences with E-value BETTER than threshold </FONT></b></CENTER>\n");
+        if (print_data->psidata->StepNumber)
+            printf("\n<IMG SRC=\"%s/blast/images/bg.gif\" WIDTH=65 HEIGHT=15>", 
+                   theInfo->www_root_path);
+        printf("                                                                     Score    E");
+        printf("\nSequences producing significant alignments:");
+        if (print_data->psidata->StepNumber)
+            printf("<IMG SRC=\"%s/blast/images/bg.gif\" WIDTH=65 HEIGHT=15>", 
+                   theInfo->www_root_path);
+        printf("                          (bits) Value\n\n");
+    }
+    
+    PrintDefLinesFromSeqAlignEx(GoodSeqAlignments, 80, stdout, 
+                                print_options, FIRST_PASS, marks, theInfo->number_of_descriptions);
+    
+    print_options -= TXALIGN_CHECK_BOX_CHECKED;
+    
+    if (print_data->psidata->StepNumber == 0)
+        printf("<a name = Evalue> </a>");
+    
+    if (theInfo->number_of_descriptions > countGood && BadSeqAlignments) {
+
+        printSubmitButton(stdout, 
+                          print_data->psidata->StepNumber+1);
+        
+        printf("<HR><CENTER><b><FONT color=\"green\">"
+               "Sequences with E-value WORSE than threshold </FONT></b></CENTER>\n");
+    
+        PrintDefLinesFromSeqAlignEx(BadSeqAlignments, 80, stdout, print_options, FIRST_PASS, &marks[countGood], theInfo->number_of_descriptions - countGood);
+    }
+
+    if (theInfo->number_of_descriptions) {
+	printSubmitButton(stdout, 
+                          print_data->psidata->StepNumber+1);
+    }
+
+    free_buff();
+    fflush(stdout);
+
+    /* merge lists */
+    if (lastGood)
+	lastGood->next = BadSeqAlignments;
+
+    prune = BlastPruneHitsFromSeqAlign((SeqAlignPtr) seqannot->data, theInfo->number_of_alignments, NULL);
+    seqannot->data = prune->sap;
+
+    fprintf(stdout, "<HR>");
+
+    txmatrix = NULL;
+    if (print_data->matrix)
+       txmatrix = (Int4Ptr PNTR) BlastMatrixToTxMatrix(print_data->matrix);
+
+    if (theInfo->number_of_alignments) {
+	fprintf(stdout, "<CENTER><b><FONT color=\"green\">"
+		"Alignments</FONT></b></CENTER>\n");
+
+        /* New DDV formating requested */
+        if(theInfo->color_schema != 0) {
+            if(!DDV_DisplayBlastPairList(prune->sap, print_data->mask_loc, 
+                                         stdout, 
+                                         theInfo->query_is_na, align_options, 
+                                         theInfo->color_schema)) { 
+                fprintf(stdout, 
+                        "\n\n!!!\n   "
+                        "    --------  Failure to print alignment...  --------"
+                        "\n!!!\n\n");
+                fflush(stdout);
+            }
+        } else {   /* Old type formating */
+            if (theInfo->align_view == Pairwise) {
+                ShowTextAlignFromAnnot2(seqannot, 60, stdout, f_order,
+                                        g_order, align_options, txmatrix, 
+                                        print_data->mask_loc, 
+                                        FormatScoreFunc, theInfo->database, 
+                                        "psiblast");
+            } else { 
+                ShowTextAlignFromAnnot2(seqannot, 60, stdout, f_order,
+                   g_order, align_options, txmatrix, print_data->mask_loc, 
+                   NULL, NULL, theInfo->www_blast_type);
+                printf("<P>\n");
+            }
+        }
+    }
+
+    /* separate lists */
+    if (lastGood)
+	lastGood->next = NULL;
+
+    fflush(stdout);
+    ObjMgrClearHold(); 
+
+    prune = BlastPruneSapStructDestruct(prune);
+
+    seqannot->data = NULL; 
+    seqannot = SeqAnnotFree(seqannot);
+
+    printf("<PRE>\n");
+
+    BlastTimeFillStructure(&time_keeper);
+
+    fprintf(stdout, "CPU time: %8.2f user secs.\t%8.2f sys. "
+	    "secs\t%8.2f total secs.\n\n", 
+	    time_keeper.user, time_keeper.system, time_keeper.total);    
+
+    print_data->matrix = BLAST_MatrixDestruct(print_data->matrix);
+    if (txmatrix)
+       txmatrix = (Int4Ptr PNTR) TxMatrixDestruct(txmatrix);
+
+    init_buff();
+    PrintDbReport(print_data->dbinfo, 70, stdout);
+    
+    if (print_data->ka_params) {
+	PrintKAParameters(print_data->ka_params->Lambda, 
+                          print_data->ka_params->K, 
+                          print_data->ka_params->H, 70, 
+                          stdout, FALSE);
+    }
+    
+    if (print_data->ka_params_gap) {
+	PrintKAParameters(print_data->ka_params_gap->Lambda, 
+                          print_data->ka_params_gap->K, 
+                          print_data->ka_params_gap->H, 
+                          70, stdout, TRUE);
+    }
+
+    PrintTildeSepLines(print_data->buffer, 70, stdout);
+    free_buff();
+    
+    fflush(stdout);
+
+    ReadDBBioseqFetchDisable();
+
+    return TRUE;
+}
diff --git a/network/wwwblast/blast.cgi b/network/wwwblast/blast.cgi
new file mode 100755
index 00000000..3e8c0521
--- /dev/null
+++ b/network/wwwblast/blast.cgi
@@ -0,0 +1,13 @@
+#!/bin/csh -f
+
+#
+# $Id: blast.cgi,v 1.1 2002/08/06 19:03:51 dondosha Exp $
+#
+
+echo "Content-type: text/html"
+echo ""
+
+#setenv DEBUG_COMMAND_LINE TRUE
+setenv BLASTDB db
+
+./blast.REAL
diff --git a/network/wwwblast/blast.html b/network/wwwblast/blast.html
new file mode 100644
index 00000000..e9805bea
--- /dev/null
+++ b/network/wwwblast/blast.html
@@ -0,0 +1,263 @@
+<!--
+/* $Id: blast.html,v 1.4 2003/05/22 16:20:45 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: blast.html,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.4 $
+*
+* File Description:
+*         Template for standalone BLAST Web page
+*
+* $Log: blast.html,v $
+* Revision 1.4  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.3  2003/05/09 17:54:38  dondosha
+* Added select menu for database genetic codes
+*
+* Revision 1.2  2003/05/05 18:14:02  dondosha
+* Uncommented discontiguous megablast options; added subsequence options
+*
+* Revision 1.1  2002/08/06 19:03:51  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/blast_form.gif" ISMAP> 
+
+<FORM ACTION="blast.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<B>Choose program to use and database to search:</B>
+<P>
+<a href="docs/blast_program.html">Program</a>
+<select name = "PROGRAM">
+    <option> blastn 
+    <option> blastp 
+    <option> blastx 
+    <option> tblastn 
+    <option> tblastx 
+</select>
+<a href="docs/blast_databases.html">Database</a>
+<select name = "DATALIB">
+    <option VALUE = "test_na_db"> test_na_db 
+    <option VALUE = "test_aa_db"> test_aa_db
+</select>
+
+<!--
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+-->
+
+<P>
+Enter sequence below in <a href="docs/fasta.html">FASTA</a>  format 
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+<P>
+Set subsequence: From
+&nbsp;&nbsp<input TYPE="text" NAME="QUERY_FROM" VALUE="" SIZE="10">
+&nbsp;&nbsp&nbsp;&nbsp To
+<input TYPE="text" NAME="QUERY_TO" VALUE="" SIZE="10">
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.QUERY_FROM.value='';MainBlastForm.QUERY_TO.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+<HR>
+
+The query sequence is 
+<a href="docs/filtered.html">filtered</a> 
+for low complexity regions by default.
+<BR>
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<a href="docs/matrix_info.html">Matrix</a>
+<select name = "MAT_PARAM">
+    <option value = "PAM30	 9	 1"> PAM30 </option>
+    <option value = "PAM70	 10	 1"> PAM70 </option> 
+    <option value = "BLOSUM80	 10	 1"> BLOSUM80 </option>
+    <option selected value = "BLOSUM62	 11	 1"> BLOSUM62 </option>
+    <option value = "BLOSUM45	 14	 2"> BLOSUM45 </option>
+</select>
+<INPUT TYPE="checkbox" NAME="UNGAPPED_ALIGNMENT" VALUE="is_set"> Perform ungapped alignment 
+<P>
+<a href="docs/newoptions.html#gencodes">Query Genetic Codes (blastx only) 
+</a>
+<select name = "GENETIC_CODE">
+ <option> Standard (1) 
+ <option> Vertebrate Mitochondrial (2) 
+ <option> Yeast Mitochondrial (3) 
+ <option> Mold Mitochondrial; ... (4) 
+ <option> Invertebrate Mitochondrial (5) 
+ <option> Ciliate Nuclear; ... (6) 
+ <option> Echinoderm Mitochondrial (9) 
+ <option> Euplotid Nuclear (10) 
+ <option> Bacterial (11) 
+ <option> Alternative Yeast Nuclear (12) 
+ <option> Ascidian Mitochondrial (13) 
+ <option> Flatworm Mitochondrial (14) 
+ <option> Blepharisma Macronuclear (15) 
+</select>
+<P>
+<a href="docs/newoptions.html#gencodes">Database Genetic Codes (tblast[nx] only)
+</a>
+<select name = "DB_GENETIC_CODE">
+ <option> Standard (1)
+ <option> Vertebrate Mitochondrial (2)
+ <option> Yeast Mitochondrial (3)
+ <option> Mold Mitochondrial; ... (4)
+ <option> Invertebrate Mitochondrial (5)
+ <option> Ciliate Nuclear; ... (6)
+ <option> Echinoderm Mitochondrial (9)
+ <option> Euplotid Nuclear (10)
+ <option> Bacterial (11)
+ <option> Alternative Yeast Nuclear (12)
+ <option> Ascidian Mitochondrial (13)
+ <option> Flatworm Mitochondrial (14)
+ <option> Blepharisma Macronuclear (15)
+</select>
+<P>
+<a href="docs/oof_notation.html">Frame shift penalty</a> for blastx 
+<select NAME = "OOF_ALIGN"> 
+ <option> 6
+ <option> 7
+ <option> 8
+ <option> 9
+ <option> 10
+ <option> 11
+ <option> 12
+ <option> 13
+ <option> 14
+ <option> 15
+ <option> 16
+ <option> 17
+ <option> 18
+ <option> 19
+ <option> 20
+ <option> 25   
+ <option> 30
+ <option> 50
+ <option> 1000
+ <option selected VALUE = "0"> No OOF
+</select>
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">
+<HR>
+<!--
+<INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp;
+-->
+<INPUT TYPE="checkbox" NAME="OVERVIEW"  CHECKED> 
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> master-slave with identities
+    <option value=2> master-slave without identities
+    <option value=3> flat master-slave with identities
+    <option value=4> flat master-slave without identities
+    <option value=7> BLAST XML
+    <option value=9> Hit Table
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option selected> 100 
+    <option> 250 
+    <option> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option selected> 50 
+    <option> 100 
+    <option> 250 
+    <option> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/blast.rc b/network/wwwblast/blast.rc
new file mode 100644
index 00000000..557915bc
--- /dev/null
+++ b/network/wwwblast/blast.rc
@@ -0,0 +1,28 @@
+# $Id: blast.rc,v 1.2 2002/12/02 21:22:32 dondosha Exp $
+#
+#================================================================
+#
+#     This is dynamic configuration file for WWW BLAST service
+#              All lines started from '#' are ignored.
+#           "//" string considered as start of comments
+#
+#     Author Sergei B. Shavirin
+#
+# $Revision: 1.2 $
+#
+#
+##################################################################
+#
+#
+# Number of CPUs to use for a single request
+#
+NumCpuToUse     4
+#
+# Here are list of combinations program/database, 
+# that allowed by BLAST service. Format: <program> <db> <db> ...
+#
+blastn test_na_db 
+blastp test_aa_db
+blastx test_aa_db
+tblastn test_na_db
+tblastx test_na_db
diff --git a/network/wwwblast/blast_cs.cgi b/network/wwwblast/blast_cs.cgi
new file mode 100755
index 00000000..3b2e7c51
--- /dev/null
+++ b/network/wwwblast/blast_cs.cgi
@@ -0,0 +1,13 @@
+#!/bin/csh -f
+
+#
+# $Id: blast_cs.cgi,v 1.1 2002/08/06 19:03:51 dondosha Exp $
+#
+
+echo "Content-type: text/html"
+echo ""
+
+#setenv DEBUG_COMMAND_LINE TRUE
+setenv BLASTDB db
+
+./blast_cs.REAL
diff --git a/network/wwwblast/blast_cs.html b/network/wwwblast/blast_cs.html
new file mode 100644
index 00000000..044e9dd2
--- /dev/null
+++ b/network/wwwblast/blast_cs.html
@@ -0,0 +1,264 @@
+<!--
+/* $Id: blast_cs.html,v 1.4 2003/05/22 16:20:45 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: blast_cs.html,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.4 $
+*
+* File Description:
+*         Template for standalone BLAST Web page
+*
+* $Log: blast_cs.html,v $
+* Revision 1.4  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.3  2003/05/09 17:54:38  dondosha
+* Added select menu for database genetic codes
+*
+* Revision 1.2  2003/05/05 18:14:02  dondosha
+* Uncommented discontiguous megablast options; added subsequence options
+*
+* Revision 1.1  2002/08/06 19:03:51  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/blast_form.gif" ISMAP> 
+
+<FORM ACTION="blast_cs.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<B>Choose program to use and database to search:</B>
+<P>
+<a href="docs/blast_program.html">Program</a>
+<select name = "PROGRAM">
+    <option> blastn 
+    <option> blastp 
+    <option> blastx 
+    <option> tblastn 
+    <option> tblastx 
+</select>
+<a href="docs/blast_databases.html">Database</a>
+<select name = "DATALIB">
+    <option VALUE = "test_na_db"> test_na_db 
+    <option VALUE = "test_aa_db"> test_aa_db
+</select>
+<P>
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+<INPUT TYPE="submit" VALUE="Search">&nbsp;&nbsp;
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.QUERY_FROM.value='';MainBlastForm.QUERY_TO.value='';MainBlastForm.SEQUENCE.focus();">
+
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+
+<P>Please read about <a href="/BLAST/fasta.html">FASTA</a> format description
+<P>
+Set subsequence: From
+&nbsp;&nbsp<input TYPE="text" NAME="QUERY_FROM" VALUE="" SIZE="10">
+&nbsp;&nbsp&nbsp;&nbsp To
+<input TYPE="text" NAME="QUERY_TO" VALUE="" SIZE="10">
+<P>
+<HR>
+
+The query sequence is 
+<a href="/BLAST/filtered.html">filtered</a> 
+for low complexity regions by default.
+<BR>
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<a href="docs/matrix_info.html">Matrix</a>
+<select name = "MAT_PARAM">
+    <option value = "PAM30	 9	 1"> PAM30 </option>
+    <option value = "PAM70	 10	 1"> PAM70 </option> 
+    <option value = "BLOSUM80	 10	 1"> BLOSUM80 </option>
+    <option selected value = "BLOSUM62	 11	 1"> BLOSUM62 </option>
+    <option value = "BLOSUM45	 14	 2"> BLOSUM45 </option>
+</select>
+<INPUT TYPE="checkbox" NAME="UNGAPPED_ALIGNMENT" VALUE="is_set"> Perform ungapped alignment 
+<P>
+<a href="docs/newoptions.html#gencodes">Query Genetic Codes (blastx only) 
+</a>
+<select name = "GENETIC_CODE">
+ <option> Standard (1) 
+ <option> Vertebrate Mitochondrial (2) 
+ <option> Yeast Mitochondrial (3) 
+ <option> Mold Mitochondrial; ... (4) 
+ <option> Invertebrate Mitochondrial (5) 
+ <option> Ciliate Nuclear; ... (6) 
+ <option> Echinoderm Mitochondrial (9) 
+ <option> Euplotid Nuclear (10) 
+ <option> Bacterial (11) 
+ <option> Alternative Yeast Nuclear (12) 
+ <option> Ascidian Mitochondrial (13) 
+ <option> Flatworm Mitochondrial (14) 
+ <option> Blepharisma Macronuclear (15) 
+</select>
+<P>
+<a href="docs/newoptions.html#gencodes">Database Genetic Codes (tblast[nx] only)
+</a>
+<select name = "DB_GENETIC_CODE">
+ <option> Standard (1)
+ <option> Vertebrate Mitochondrial (2)
+ <option> Yeast Mitochondrial (3)
+ <option> Mold Mitochondrial; ... (4)
+ <option> Invertebrate Mitochondrial (5)
+ <option> Ciliate Nuclear; ... (6)
+ <option> Echinoderm Mitochondrial (9)
+ <option> Euplotid Nuclear (10)
+ <option> Bacterial (11)
+ <option> Alternative Yeast Nuclear (12)
+ <option> Ascidian Mitochondrial (13)
+ <option> Flatworm Mitochondrial (14)
+ <option> Blepharisma Macronuclear (15)
+</select>
+<P>
+<a href="docs/oof_notation.html">Frame shift penalty</a> for blastx 
+<select NAME = "OOF_ALIGN"> 
+ <option> 6
+ <option> 7
+ <option> 8
+ <option> 9
+ <option> 10
+ <option> 11
+ <option> 12
+ <option> 13
+ <option> 14
+ <option> 15
+ <option> 16
+ <option> 17
+ <option> 18
+ <option> 19
+ <option> 20
+ <option> 25   
+ <option> 30
+ <option> 50
+ <option> 1000
+ <option selected VALUE = "0"> No OOF
+</select>
+<P>
+Limit search to results of <a href="http://www.ncbi.nlm.nih.gov/entrez/query/static/help/helpdoc.html#Writing_Advanced_Search_Statements">Entrez query</a> <INPUT TYPE="text" NAME = "ENTREZ_QUERY" MAXLENGTH="50">
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">&nbsp;
+<INPUT TYPE="checkbox" NAME="TAX_BLAST"> Show <a href ="docs/taxblasthelp.html">Tax Blast reports</a>
+<HR>
+
+<INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp;
+
+<INPUT TYPE="checkbox" NAME="OVERVIEW"  CHECKED> 
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> master-slave with identities
+    <option value=2> master-slave without identities
+    <option value=3> flat master-slave with identities
+    <option value=4> flat master-slave without identities
+    <option value=7> BLAST XML
+    <option value=8> Hit Table
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option selected> 100 
+    <option> 250 
+    <option> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option selected> 50 
+    <option> 100 
+    <option> 250 
+    <option> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/config_setup.pl b/network/wwwblast/config_setup.pl
new file mode 100644
index 00000000..8fe0533b
--- /dev/null
+++ b/network/wwwblast/config_setup.pl
@@ -0,0 +1,132 @@
+#!/usr/local/bin/perl
+
+# make_config_files.pl
+#
+# the purpose of this script is to make it easier to set up the
+# Standalone WWW Blast server.
+#
+# this script accepts as arguments a directory with formatted databases
+# and a temporary directory (where it will write output files). for example
+#
+#   make_config_files.pl $BLASTDB out
+#
+# It then creates a blast.rc and a psiblast.rc file in this temporary 
+# directory.  It also creates blastdb_options.html and 
+# psiblastdb_options.html files in this directory.
+# The blast.rc and psiblast.rc files can just replace the ones 
+# in the blast directory.  You can then cut and paste the 
+# <option> entries from the html files into the corresponding place
+# in the blast.html, blast_cs.html, xmlblast.html, megablast.html, 
+# psiblast.html, and psiblast_cs.html 
+# (overwriting the test_aa_db and test_na_db <options>)
+# 
+# you may want to adjust the default number of processors in the rc files.
+#
+# finally you will probably want to create a symbolic link from the 
+# blast database directory that you passed to this script to the
+# db directory that currently contains the test_aa_db and test_na_db
+# files.  Assuming you are in the blast directory created by the 
+# blast server distribution, the following should work:
+# 
+#    mv db db.orig
+#    ln -s $BLASTDB db
+# 
+# Author: Joseph Ryan <jfryan@nhgri.nih.gov>
+#
+
+use strict;
+use vars qw($VERSION);
+
+$VERSION = 0.01;
+
+MAIN: {
+    my $blastdb = $ARGV[0] or die "usage: $0 BLASTDB OUTPUT_DIR\n";
+    my $output_dir = $ARGV[1] or die "usage:$0 BLASTDB OUTPUT_DIR\n";
+    unless (-d $output_dir) {
+        mkdir $output_dir, 0755 or die "cannot mkdir $output_dir:$!";
+    }
+    my ($ra_nts,$ra_aas) = get_dbs($blastdb);
+    print_blast_html($output_dir,$ra_nts,$ra_aas);
+    print_psiblast_config($output_dir,$ra_aas);
+    print_blast_config($output_dir,$ra_nts,$ra_aas);
+    print_psiblast_html($output_dir,$ra_aas);
+    print "Four files were created in the directory: $output_dir\n";
+}
+
+sub print_psiblast_config {
+    my $output_dir = shift;
+    my $ra_aas     = shift;
+    open OUT, ">$output_dir/psiblast.rc" 
+         or die "cannot open >$output_dir/psiblast.rc:$!";
+    print OUT "NumCpuToUse     4\n\n";
+    print OUT "blastp ";
+    foreach my $aa (@{$ra_aas}) {
+        print OUT "$aa ";
+    }
+    print OUT "\n";
+}
+
+sub print_blast_config {
+    my $output_dir = shift;
+    my $ra_nts     = shift;
+    my $ra_aas     = shift;
+    open OUT, ">$output_dir/blast.rc" 
+         or die "cannot open >$output_dir/blast.rc:$!";
+    print OUT "NumCpuToUse     4\n\n";
+    foreach my $p ("blastn", "tblastn", "tblastx") {
+        print OUT "$p ";
+        foreach my $nt (@{$ra_nts}) {
+            print OUT "$nt ";
+        }
+        print OUT "\n";
+    }
+    foreach my $p ("blastp", "blastx") {
+        print OUT "$p ";
+        foreach my $aa (@{$ra_aas}) {
+            print OUT "$aa ";
+        }
+        print OUT "\n";
+    }
+}
+
+sub print_psiblast_html {
+    my $dir    = shift;
+    my $ra_aas = shift;
+    open OUT, ">$dir/psiblastdb_options.html" 
+         or die "cannot open >$dir/psiblastdb_options.html:$!";
+    foreach my $aa (@{$ra_aas}) {
+        print OUT "    <option>$aa\n";
+    }
+}
+
+sub print_blast_html {
+    my $dir    = shift;
+    my $ra_nts = shift; 
+    my $ra_aas = shift;
+    my %redundants = ();
+    open OUT, ">$dir/blastdb_options.html" 
+         or die "cannot open $dir/blastdb_options.html:$!";
+    my @dbs = sort @{$ra_nts}, @{$ra_aas};
+    foreach my $db (@dbs) {
+        next if $redundants{$db};
+        print OUT "    <option>$db\n";
+        $redundants{$db}++;
+    }
+}
+
+sub get_dbs {
+    my $dir = shift;
+    my @nts = ();
+    my @aas = ();
+
+    opendir DIR, $dir or die "cannot open $dir:$!";
+    my @files = grep /\.[np]in$/, readdir DIR;
+    foreach my $f (@files) {
+        $f =~ m/(.*)\.([pn])in$/;
+        push @nts, $1 if ($2 eq 'n');
+        push @aas, $1 if ($2 eq 'p');
+    }
+    return \@nts, \@aas;
+}
+
+
diff --git a/network/wwwblast/data/BLOSUM45 b/network/wwwblast/data/BLOSUM45
new file mode 100644
index 00000000..18c33238
--- /dev/null
+++ b/network/wwwblast/data/BLOSUM45
@@ -0,0 +1,31 @@
+#  Matrix made by matblas from blosum45.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 45
+#  Entropy =   0.3795, Expected =  -0.2789
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  5 -2 -1 -2 -1 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -2 -2  0 -1 -1  0 -5 
+R -2  7  0 -1 -3  1  0 -2  0 -3 -2  3 -1 -2 -2 -1 -1 -2 -1 -2 -1  0 -1 -5 
+N -1  0  6  2 -2  0  0  0  1 -2 -3  0 -2 -2 -2  1  0 -4 -2 -3  4  0 -1 -5 
+D -2 -1  2  7 -3  0  2 -1  0 -4 -3  0 -3 -4 -1  0 -1 -4 -2 -3  5  1 -1 -5 
+C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5 
+Q -1  1  0  0 -3  6  2 -2  1 -2 -2  1  0 -4 -1  0 -1 -2 -1 -3  0  4 -1 -5 
+E -1  0  0  2 -3  2  6 -2  0 -3 -2  1 -2 -3  0  0 -1 -3 -2 -3  1  4 -1 -5 
+G  0 -2  0 -1 -3 -2 -2  7 -2 -4 -3 -2 -2 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -5 
+H -2  0  1  0 -3  1  0 -2 10 -3 -2 -1  0 -2 -2 -1 -2 -3  2 -3  0  0 -1 -5 
+I -1 -3 -2 -4 -3 -2 -3 -4 -3  5  2 -3  2  0 -2 -2 -1 -2  0  3 -3 -3 -1 -5 
+L -1 -2 -3 -3 -2 -2 -2 -3 -2  2  5 -3  2  1 -3 -3 -1 -2  0  1 -3 -2 -1 -5 
+K -1  3  0  0 -3  1  1 -2 -1 -3 -3  5 -1 -3 -1 -1 -1 -2 -1 -2  0  1 -1 -5 
+M -1 -1 -2 -3 -2  0 -2 -2  0  2  2 -1  6  0 -2 -2 -1 -2  0  1 -2 -1 -1 -5 
+F -2 -2 -2 -4 -2 -4 -3 -3 -2  0  1 -3  0  8 -3 -2 -1  1  3  0 -3 -3 -1 -5 
+P -1 -2 -2 -1 -4 -1  0 -2 -2 -2 -3 -1 -2 -3  9 -1 -1 -3 -3 -3 -2 -1 -1 -5 
+S  1 -1  1  0 -1  0  0  0 -1 -2 -3 -1 -2 -2 -1  4  2 -4 -2 -1  0  0  0 -5 
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1  2  5 -3 -1  0  0 -1  0 -5 
+W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2  1 -3 -4 -3 15  3 -3 -4 -2 -2 -5 
+Y -2 -1 -2 -2 -3 -1 -2 -3  2  0  0 -1  0  3 -3 -2 -1  3  8 -1 -2 -2 -1 -5 
+V  0 -2 -3 -3 -1 -3 -3 -3 -3  3  1 -2  1  0 -3 -1  0 -3 -1  5 -3 -3 -1 -5 
+B -1 -1  4  5 -2  0  1 -1  0 -3 -3  0 -2 -3 -2  0  0 -4 -2 -3  4  2 -1 -5 
+Z -1  0  0  1 -3  4  4 -2  0 -3 -2  1 -1 -3 -1  0 -1 -2 -2 -3  2  4 -1 -5 
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1  0  0 -2 -1 -1 -1 -1 -1 -5 
+* -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5  1 
diff --git a/network/wwwblast/data/BLOSUM62 b/network/wwwblast/data/BLOSUM62
new file mode 100644
index 00000000..205f139a
--- /dev/null
+++ b/network/wwwblast/data/BLOSUM62
@@ -0,0 +1,31 @@
+#  Matrix made by matblas from blosum62.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 62
+#  Entropy =   0.6979, Expected =  -0.5209
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *
+A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 
+R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 
+N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 
+D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 
+C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 
+Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 
+E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 
+H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 
+I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 
+L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 
+K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 
+M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 
+F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 
+P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 
+S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 
+W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 
+Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 
+V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 
+B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 
+Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 
+X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 
+* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 
diff --git a/network/wwwblast/data/BLOSUM80 b/network/wwwblast/data/BLOSUM80
new file mode 100644
index 00000000..18f6cea8
--- /dev/null
+++ b/network/wwwblast/data/BLOSUM80
@@ -0,0 +1,31 @@
+#  Matrix made by matblas from blosum80.iij
+#  * column uses minimum score
+#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units
+#  Blocks Database = /data/blocks_5.0/blocks.dat
+#  Cluster Percentage: >= 80
+#  Entropy =   0.9868, Expected =  -0.7442
+   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *  
+A  5 -2 -2 -2 -1 -1 -1  0 -2 -2 -2 -1 -1 -3 -1  1  0 -3 -2  0 -2 -1 -1 -6 
+R -2  6 -1 -2 -4  1 -1 -3  0 -3 -3  2 -2 -4 -2 -1 -1 -4 -3 -3 -2  0 -1 -6 
+N -2 -1  6  1 -3  0 -1 -1  0 -4 -4  0 -3 -4 -3  0  0 -4 -3 -4  4  0 -1 -6 
+D -2 -2  1  6 -4 -1  1 -2 -2 -4 -5 -1 -4 -4 -2 -1 -1 -6 -4 -4  4  1 -2 -6 
+C -1 -4 -3 -4  9 -4 -5 -4 -4 -2 -2 -4 -2 -3 -4 -2 -1 -3 -3 -1 -4 -4 -3 -6 
+Q -1  1  0 -1 -4  6  2 -2  1 -3 -3  1  0 -4 -2  0 -1 -3 -2 -3  0  3 -1 -6 
+E -1 -1 -1  1 -5  2  6 -3  0 -4 -4  1 -2 -4 -2  0 -1 -4 -3 -3  1  4 -1 -6 
+G  0 -3 -1 -2 -4 -2 -3  6 -3 -5 -4 -2 -4 -4 -3 -1 -2 -4 -4 -4 -1 -3 -2 -6 
+H -2  0  0 -2 -4  1  0 -3  8 -4 -3 -1 -2 -2 -3 -1 -2 -3  2 -4 -1  0 -2 -6 
+I -2 -3 -4 -4 -2 -3 -4 -5 -4  5  1 -3  1 -1 -4 -3 -1 -3 -2  3 -4 -4 -2 -6 
+L -2 -3 -4 -5 -2 -3 -4 -4 -3  1  4 -3  2  0 -3 -3 -2 -2 -2  1 -4 -3 -2 -6 
+K -1  2  0 -1 -4  1  1 -2 -1 -3 -3  5 -2 -4 -1 -1 -1 -4 -3 -3 -1  1 -1 -6 
+M -1 -2 -3 -4 -2  0 -2 -4 -2  1  2 -2  6  0 -3 -2 -1 -2 -2  1 -3 -2 -1 -6 
+F -3 -4 -4 -4 -3 -4 -4 -4 -2 -1  0 -4  0  6 -4 -3 -2  0  3 -1 -4 -4 -2 -6 
+P -1 -2 -3 -2 -4 -2 -2 -3 -3 -4 -3 -1 -3 -4  8 -1 -2 -5 -4 -3 -2 -2 -2 -6 
+S  1 -1  0 -1 -2  0  0 -1 -1 -3 -3 -1 -2 -3 -1  5  1 -4 -2 -2  0  0 -1 -6 
+T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -2 -1 -1 -2 -2  1  5 -4 -2  0 -1 -1 -1 -6 
+W -3 -4 -4 -6 -3 -3 -4 -4 -3 -3 -2 -4 -2  0 -5 -4 -4 11  2 -3 -5 -4 -3 -6 
+Y -2 -3 -3 -4 -3 -2 -3 -4  2 -2 -2 -3 -2  3 -4 -2 -2  2  7 -2 -3 -3 -2 -6 
+V  0 -3 -4 -4 -1 -3 -3 -4 -4  3  1 -3  1 -1 -3 -2  0 -3 -2  4 -4 -3 -1 -6 
+B -2 -2  4  4 -4  0  1 -1 -1 -4 -4 -1 -3 -4 -2  0 -1 -5 -3 -4  4  0 -2 -6 
+Z -1  0  0  1 -4  3  4 -3  0 -4 -3  1 -2 -4 -2  0 -1 -4 -3 -3  0  4 -1 -6 
+X -1 -1 -1 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -1 -6 
+* -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6  1 
diff --git a/network/wwwblast/data/PAM30 b/network/wwwblast/data/PAM30
new file mode 100644
index 00000000..8a01c886
--- /dev/null
+++ b/network/wwwblast/data/PAM30
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 30 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -5.06, Entropy = 2.57 bits
+#
+# Lowest score = -17, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   6  -7  -4  -3  -6  -4  -2  -2  -7  -5  -6  -7  -5  -8  -2   0  -1 -13  -8  -2  -3  -3  -3 -17
+R  -7   8  -6 -10  -8  -2  -9  -9  -2  -5  -8   0  -4  -9  -4  -3  -6  -2 -10  -8  -7  -4  -6 -17
+N  -4  -6   8   2 -11  -3  -2  -3   0  -5  -7  -1  -9  -9  -6   0  -2  -8  -4  -8   6  -3  -3 -17
+D  -3 -10   2   8 -14  -2   2  -3  -4  -7 -12  -4 -11 -15  -8  -4  -5 -15 -11  -8   6   1  -5 -17
+C  -6  -8 -11 -14  10 -14 -14  -9  -7  -6 -15 -14 -13 -13  -8  -3  -8 -15  -4  -6 -12 -14  -9 -17
+Q  -4  -2  -3  -2 -14   8   1  -7   1  -8  -5  -3  -4 -13  -3  -5  -5 -13 -12  -7  -3   6  -5 -17
+E  -2  -9  -2   2 -14   1   8  -4  -5  -5  -9  -4  -7 -14  -5  -4  -6 -17  -8  -6   1   6  -5 -17
+G  -2  -9  -3  -3  -9  -7  -4   6  -9 -11 -10  -7  -8  -9  -6  -2  -6 -15 -14  -5  -3  -5  -5 -17
+H  -7  -2   0  -4  -7   1  -5  -9   9  -9  -6  -6 -10  -6  -4  -6  -7  -7  -3  -6  -1  -1  -5 -17
+I  -5  -5  -5  -7  -6  -8  -5 -11  -9   8  -1  -6  -1  -2  -8  -7  -2 -14  -6   2  -6  -6  -5 -17
+L  -6  -8  -7 -12 -15  -5  -9 -10  -6  -1   7  -8   1  -3  -7  -8  -7  -6  -7  -2  -9  -7  -6 -17
+K  -7   0  -1  -4 -14  -3  -4  -7  -6  -6  -8   7  -2 -14  -6  -4  -3 -12  -9  -9  -2  -4  -5 -17
+M  -5  -4  -9 -11 -13  -4  -7  -8 -10  -1   1  -2  11  -4  -8  -5  -4 -13 -11  -1 -10  -5  -5 -17
+F  -8  -9  -9 -15 -13 -13 -14  -9  -6  -2  -3 -14  -4   9 -10  -6  -9  -4   2  -8 -10 -13  -8 -17
+P  -2  -4  -6  -8  -8  -3  -5  -6  -4  -8  -7  -6  -8 -10   8  -2  -4 -14 -13  -6  -7  -4  -5 -17
+S   0  -3   0  -4  -3  -5  -4  -2  -6  -7  -8  -4  -5  -6  -2   6   0  -5  -7  -6  -1  -5  -3 -17
+T  -1  -6  -2  -5  -8  -5  -6  -6  -7  -2  -7  -3  -4  -9  -4   0   7 -13  -6  -3  -3  -6  -4 -17
+W -13  -2  -8 -15 -15 -13 -17 -15  -7 -14  -6 -12 -13  -4 -14  -5 -13  13  -5 -15 -10 -14 -11 -17
+Y  -8 -10  -4 -11  -4 -12  -8 -14  -3  -6  -7  -9 -11   2 -13  -7  -6  -5  10  -7  -6  -9  -7 -17
+V  -2  -8  -8  -8  -6  -7  -6  -5  -6   2  -2  -9  -1  -8  -6  -6  -3 -15  -7   7  -8  -6  -5 -17
+B  -3  -7   6   6 -12  -3   1  -3  -1  -6  -9  -2 -10 -10  -7  -1  -3 -10  -6  -8   6   0  -5 -17
+Z  -3  -4  -3   1 -14   6   6  -5  -1  -6  -7  -4  -5 -13  -4  -5  -6 -14  -9  -6   0   6  -5 -17
+X  -3  -6  -3  -5  -9  -5  -5  -5  -5  -5  -6  -5  -5  -8  -5  -3  -4 -11  -7  -5  -5  -5  -5 -17
+* -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17   1
diff --git a/network/wwwblast/data/PAM70 b/network/wwwblast/data/PAM70
new file mode 100644
index 00000000..b20cdf08
--- /dev/null
+++ b/network/wwwblast/data/PAM70
@@ -0,0 +1,34 @@
+#
+# This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+#
+# PAM 70 substitution matrix, scale = ln(2)/2 = 0.346574
+#
+# Expected score = -2.77, Entropy = 1.60 bits
+#
+# Lowest score = -11, Highest score = 13
+#
+    A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+A   5  -4  -2  -1  -4  -2  -1   0  -4  -2  -4  -4  -3  -6   0   1   1  -9  -5  -1  -1  -1  -2 -11
+R  -4   8  -3  -6  -5   0  -5  -6   0  -3  -6   2  -2  -7  -2  -1  -4   0  -7  -5  -4  -2  -3 -11
+N  -2  -3   6   3  -7  -1   0  -1   1  -3  -5   0  -5  -6  -3   1   0  -6  -3  -5   5  -1  -2 -11
+D  -1  -6   3   6  -9   0   3  -1  -1  -5  -8  -2  -7 -10  -4  -1  -2 -10  -7  -5   5   2  -3 -11
+C  -4  -5  -7  -9   9  -9  -9  -6  -5  -4 -10  -9  -9  -8  -5  -1  -5 -11  -2  -4  -8  -9  -6 -11
+Q  -2   0  -1   0  -9   7   2  -4   2  -5  -3  -1  -2  -9  -1  -3  -3  -8  -8  -4  -1   5  -2 -11
+E  -1  -5   0   3  -9   2   6  -2  -2  -4  -6  -2  -4  -9  -3  -2  -3 -11  -6  -4   2   5  -3 -11
+G   0  -6  -1  -1  -6  -4  -2   6  -6  -6  -7  -5  -6  -7  -3   0  -3 -10  -9  -3  -1  -3  -3 -11
+H  -4   0   1  -1  -5   2  -2  -6   8  -6  -4  -3  -6  -4  -2  -3  -4  -5  -1  -4   0   1  -3 -11
+I  -2  -3  -3  -5  -4  -5  -4  -6  -6   7   1  -4   1   0  -5  -4  -1  -9  -4   3  -4  -4  -3 -11
+L  -4  -6  -5  -8 -10  -3  -6  -7  -4   1   6  -5   2  -1  -5  -6  -4  -4  -4   0  -6  -4  -4 -11
+K  -4   2   0  -2  -9  -1  -2  -5  -3  -4  -5   6   0  -9  -4  -2  -1  -7  -7  -6  -1  -2  -3 -11
+M  -3  -2  -5  -7  -9  -2  -4  -6  -6   1   2   0  10  -2  -5  -3  -2  -8  -7   0  -6  -3  -3 -11
+F  -6  -7  -6 -10  -8  -9  -9  -7  -4   0  -1  -9  -2   8  -7  -4  -6  -2   4  -5  -7  -9  -5 -11
+P   0  -2  -3  -4  -5  -1  -3  -3  -2  -5  -5  -4  -5  -7   7   0  -2  -9  -9  -3  -4  -2  -3 -11
+S   1  -1   1  -1  -1  -3  -2   0  -3  -4  -6  -2  -3  -4   0   5   2  -3  -5  -3   0  -2  -1 -11
+T   1  -4   0  -2  -5  -3  -3  -3  -4  -1  -4  -1  -2  -6  -2   2   6  -8  -4  -1  -1  -3  -2 -11
+W  -9   0  -6 -10 -11  -8 -11 -10  -5  -9  -4  -7  -8  -2  -9  -3  -8  13  -3 -10  -7 -10  -7 -11
+Y  -5  -7  -3  -7  -2  -8  -6  -9  -1  -4  -4  -7  -7   4  -9  -5  -4  -3   9  -5  -4  -7  -5 -11
+V  -1  -5  -5  -5  -4  -4  -4  -3  -4   3   0  -6   0  -5  -3  -3  -1 -10  -5   6  -5  -4  -2 -11
+B  -1  -4   5   5  -8  -1   2  -1   0  -4  -6  -1  -6  -7  -4   0  -1  -7  -4  -5   5   1  -2 -11
+Z  -1  -2  -1   2  -9   5   5  -3   1  -4  -4  -2  -3  -9  -2  -2  -3 -10  -7  -4   1   5  -3 -11
+X  -2  -3  -2  -3  -6  -2  -3  -3  -3  -3  -4  -3  -3  -5  -3  -1  -2  -7  -5  -2  -2  -3  -3 -11
+* -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11 -11   1
diff --git a/network/wwwblast/db/CDD/14_3_3.csq b/network/wwwblast/db/CDD/14_3_3.csq
new file mode 100644
index 00000000..cdb262d0
--- /dev/null
+++ b/network/wwwblast/db/CDD/14_3_3.csq
@@ -0,0 +1,5 @@
+>gnl|Smart|14_3_3 14-3-3 homologues; 14-3-3 homologues mediates signal transduction by binding to phosphoserine-containing proteins. They are involved in growth factor signalling and also interact with MEK kinases
+RDEYVYKAKLAEQAERYDEMAEAMKNLVENCLDEQQPKDELSVEERNLLSVAYKNAVGARRASWRIISSVEQKELSKQHM
+QNKALAAEYRQKVEEELNKICHDILQLLTDKLIPKTSDSESKVFYYKMKGDYYRYISEFSGEEGKKQAADQAQESYQKAT
+ETAEGHSPATHPIRLGLALNYSVFFYEILNLPQQACEMAKRAFDDAITEFDNVSEDSYKDSTLIMQLLRDNLTLWTSDLQ
+ADQQQQEGG
diff --git a/network/wwwblast/db/CDD/14_3_3.mtx b/network/wwwblast/db/CDD/14_3_3.mtx
new file mode 100644
index 00000000..14b39dfc
--- /dev/null
+++ b/network/wwwblast/db/CDD/14_3_3.mtx
@@ -0,0 +1,263 @@
+249
+RDEYVYKAKLAEQAERYDEMAEAMKNLVENCLDEQQPKDELSVEERNLLSVAYKNAVGARRASWRIISSVEQKELSKQHMQNKALAAEYRQKVEEELNKICHDILQLLTDKLIPKTSDSESKVFYYKMKGDYYRYISEFSGEEGKKQAADQAQESYQKATETAEGHSPATHPIRLGLALNYSVFFYEILNLPQQACEMAKRAFDDAITEFDNVSEDSYKDSTLIMQLLRDNLTLWTSDLQADQQQQEGG
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+4.468556e-02
+-3.108105e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
+-32768  -1  -32768  -3  -2  0  -3  -2  0  -3  2  -2  -1  0  -2  1  5  -1  -1  -3  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -3  4  4  -3  -1  -1  -3  0  -3  -2  0  -1  1  -1  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -4  2  5  -3  -2  0  -3  1  -3  -2  0  -1  2  0  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -2  -32768  -2  0  -1  1  -1  1  -2  -1  -2  -1  4  -2  -1  -1  0  -1  -2  0  -1  5  -32768  -32768  -32768  
+-32768  0  -32768  -1  -3  -2  -1  -3  -3  3  -2  1  1  -3  -2  -2  -3  -2  0  4  -3  -1  -1  -32768  -32768  -32768  
+-32768  -2  -32768  -2  -3  -2  3  -3  2  -1  -2  -1  -1  -2  -3  -1  -2  -2  -2  -1  2  -1  6  -32768  -32768  -32768  
+-32768  -1  -32768  -2  -2  0  -1  -2  -1  0  3  0  4  -1  -1  0  1  -1  -1  0  -2  -1  -1  -32768  -32768  -32768  
+-32768  4  -32768  0  -2  -1  -2  0  -2  -1  -1  -1  -1  -2  -1  -1  -1  1  0  0  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -3  -1  1  -3  -2  -1  -3  5  -2  -1  0  -1  1  2  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -1  -4  -3  0  -4  -3  2  -2  4  2  -3  -3  -2  -2  -2  -1  1  -2  -1  -1  -32768  -32768  -32768  
+-32768  4  -32768  0  -2  -1  -2  0  -2  -1  -1  -1  -1  -2  -1  -1  -1  1  0  0  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -4  2  5  -3  -2  0  -3  1  -3  -2  0  -1  2  0  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -3  0  2  -3  -2  0  -3  1  -2  0  0  -1  5  1  0  -1  -2  -2  -1  -1  -32768  -32768  -32768  
+-32768  4  -32768  0  -2  -1  -2  0  -2  -1  -1  -1  -1  -2  -1  -1  -1  1  0  0  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -4  2  5  -3  -2  0  -3  1  -3  -2  0  -1  2  0  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -3  -2  0  -3  -2  0  -3  2  -2  -1  0  -2  1  5  -1  -1  -3  -3  -1  -2  -32768  -32768  -32768  
+-32768  -2  -32768  -2  -3  -2  3  -3  2  -1  -2  -1  -1  -2  -3  -1  -2  -2  -2  -1  2  -1  6  -32768  -32768  -32768  
+-32768  -1  -32768  -3  4  4  -3  -1  -1  -3  0  -3  -2  0  -1  1  -1  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -4  2  5  -3  -2  0  -3  1  -3  -2  0  -1  2  0  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -1  -3  -2  0  -3  -2  1  -1  2  5  -2  -2  0  -1  -1  -1  1  -1  -1  -1  -32768  -32768  -32768  
+-32768  2  -32768  -1  -2  -1  -1  -1  -2  1  -1  0  0  -2  -1  -1  -2  0  0  3  -3  -1  -1  -32768  -32768  -32768  
+-32768  -1  -32768  -4  2  5  -3  -2  0  -3  1  -3  -2  0  -1  2  0  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  2  -32768  -1  -2  -2  4  -1  -1  -1  -2  -1  -1  -2  -2  -2  -2  0  -1  -1  0  -1  1  -32768  -32768  -32768  
+-32768  -1  -32768  -1  -3  -2  0  -3  -2  1  -1  2  5  -2  -2  0  -1  -1  -1  1  -1  -1  -1  -32768  -32768  -32768  
+-32768  -1  -32768  -3  1  3  -3  -2  -1  -3  3  -2  -1  0  -1  1  1  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -3  0  0  -3  -1  0  -3  3  -2  -1  4  -1  0  1  0  -1  -2  -3  -1  -2  -32768  -32768  -32768  
+-32768  -1  -32768  -1  -3  -2  -1  -3  -3  2  -2  3  1  -3  -2  -2  -2  -2  -1  3  -2  -1  -1  -32768  -32768  -32768  
+-32768  0  -32768  -1  -1  -1  -1  -1  -2  1  -1  0  0  0  -1  -1  -2  2  0  2  -3  -1  -1  -32768  -32768  -32768  
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diff --git a/network/wwwblast/db/CDD/35EXOc.csq b/network/wwwblast/db/CDD/35EXOc.csq
new file mode 100644
index 00000000..1e726e8b
--- /dev/null
+++ b/network/wwwblast/db/CDD/35EXOc.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|35EXOc 3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
+YVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLL
+EDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQI
+ALEEAGRYAAEDADVTLQLHLKMWPDLQ
diff --git a/network/wwwblast/db/CDD/35EXOc.mtx b/network/wwwblast/db/CDD/35EXOc.mtx
new file mode 100644
index 00000000..b5dda94a
--- /dev/null
+++ b/network/wwwblast/db/CDD/35EXOc.mtx
@@ -0,0 +1,202 @@
+188
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+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/4.1m.csq b/network/wwwblast/db/CDD/4.1m.csq
new file mode 100644
index 00000000..c3efd160
--- /dev/null
+++ b/network/wwwblast/db/CDD/4.1m.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|4.1m putative band 4.1 homologues' binding motif
+MYKYRNRDEGSYHVDESRN
diff --git a/network/wwwblast/db/CDD/4.1m.mtx b/network/wwwblast/db/CDD/4.1m.mtx
new file mode 100644
index 00000000..00a6b4e6
--- /dev/null
+++ b/network/wwwblast/db/CDD/4.1m.mtx
@@ -0,0 +1,33 @@
+19
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diff --git a/network/wwwblast/db/CDD/53EXOc.csq b/network/wwwblast/db/CDD/53EXOc.csq
new file mode 100644
index 00000000..eef8b42e
--- /dev/null
+++ b/network/wwwblast/db/CDD/53EXOc.csq
@@ -0,0 +1,5 @@
+>gnl|Smart|53EXOc 5'-3' exonuclease
+RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKA
+LDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRD
+MYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLIL
+VDLPTYCVDAIAAVG
diff --git a/network/wwwblast/db/CDD/53EXOc.mtx b/network/wwwblast/db/CDD/53EXOc.mtx
new file mode 100644
index 00000000..0b91a5ea
--- /dev/null
+++ b/network/wwwblast/db/CDD/53EXOc.mtx
@@ -0,0 +1,269 @@
+255
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diff --git a/network/wwwblast/db/CDD/A1pp.csq b/network/wwwblast/db/CDD/A1pp.csq
new file mode 100644
index 00000000..fb45bb8c
--- /dev/null
+++ b/network/wwwblast/db/CDD/A1pp.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|A1pp Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson & Fuji)
+RFHCFKGHFSHDKILNKKSGAVVISSHSSMDFSTTLGRAFAVTTCLQRSCWEKIKNNIPTPEKHLPIGSCVSGPWDVEEG
+AQLYTSHLIVINPPTLETLIKEKMRRAITLKDFSMKEAFTNLVLAYLQCFDICIEHNLESVQLEVFGLNNLSADQEEFTT
+WE
diff --git a/network/wwwblast/db/CDD/A1pp.mtx b/network/wwwblast/db/CDD/A1pp.mtx
new file mode 100644
index 00000000..d6c875f0
--- /dev/null
+++ b/network/wwwblast/db/CDD/A1pp.mtx
@@ -0,0 +1,176 @@
+162
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+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.186137e-02
+-2.959181e+00
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+1.340000e-01
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diff --git a/network/wwwblast/db/CDD/A4_EXTRA.csq b/network/wwwblast/db/CDD/A4_EXTRA.csq
new file mode 100644
index 00000000..981a5f5d
--- /dev/null
+++ b/network/wwwblast/db/CDD/A4_EXTRA.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|A4_EXTRA amyloid A4; amyloid A4 precursor of Alzheimers disease
+QAASPRWEPQIAVLCEAGQIYQPQYLSEEGRWVTDLSKKTTGPTCLRDKMDLLDYCKKAYPNRDITNIVESSHYQKIGGW
+CRQGALNAAKCKGSHRWIKPFRCLGPFQSDALLVPEGCLFDHIHNASRCWPFVRWNQTGAAACQERGMQMRTFAMLLPCG
+ISVFSGVEFVCCP
diff --git a/network/wwwblast/db/CDD/A4_EXTRA.mtx b/network/wwwblast/db/CDD/A4_EXTRA.mtx
new file mode 100644
index 00000000..f05111e6
--- /dev/null
+++ b/network/wwwblast/db/CDD/A4_EXTRA.mtx
@@ -0,0 +1,187 @@
+173
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+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/AAA.csq b/network/wwwblast/db/CDD/AAA.csq
new file mode 100644
index 00000000..6963373c
--- /dev/null
+++ b/network/wwwblast/db/CDD/AAA.csq
@@ -0,0 +1,5 @@
+>gnl|Smart|AAA ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment
+TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKMVRVQAIEKNRYRAEELAE
+ERILDVLIPPAKNNWGQTEQQQEPSAARQAFRKKLREGQLDDKEIEIDLAAAPMGVEIMAPPGMEEMTSQLQSMFQNLGG
+QKQKARKLKIKDAMKLLIEEEAAKLVNPEELKQDAIDAVEQHGIVFIDEIDKICKRGESSGPDVSREGVQRDLLPLVEGC
+TVSTKHGMVKTDHILFIASGAFQIAKPSDLIPELQGRLPIRVEL
diff --git a/network/wwwblast/db/CDD/AAA.mtx b/network/wwwblast/db/CDD/AAA.mtx
new file mode 100644
index 00000000..8e728b58
--- /dev/null
+++ b/network/wwwblast/db/CDD/AAA.mtx
@@ -0,0 +1,298 @@
+284
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+2.700000e-01
+4.700000e-02
+-3.057608e+00
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+-3.469035e+00
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diff --git a/network/wwwblast/db/CDD/AAI.csq b/network/wwwblast/db/CDD/AAI.csq
new file mode 100644
index 00000000..3ba8c076
--- /dev/null
+++ b/network/wwwblast/db/CDD/AAI.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|AAI Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family
+CYPGQAFQVPALPACRPLLRLQCNGSQVPEAVLRDCCQQLAHISEWCRCGALYSMLDSMYKEHGAQEGQAGTGAFPRCRR
+EVVKLTAASITAVCRLPIVVDASGDGAYVC
diff --git a/network/wwwblast/db/CDD/AAI.mtx b/network/wwwblast/db/CDD/AAI.mtx
new file mode 100644
index 00000000..cc015873
--- /dev/null
+++ b/network/wwwblast/db/CDD/AAI.mtx
@@ -0,0 +1,124 @@
+110
+CYPGQAFQVPALPACRPLLRLQCNGSQVPEAVLRDCCQQLAHISEWCRCGALYSMLDSMYKEHGAQEGQAGTGAFPRCRREVVKLTAASITAVCRLPIVVDASGDGAYVC
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+3.730677e-02
+-3.288580e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/ACTIN.csq b/network/wwwblast/db/CDD/ACTIN.csq
new file mode 100644
index 00000000..12a0d122
--- /dev/null
+++ b/network/wwwblast/db/CDD/ACTIN.csq
@@ -0,0 +1,6 @@
+>gnl|Smart|ACTIN Actin; ACTIN subfamily of ACTIN/mreB/sugarkinase/Hsp70 superfamily
+VQALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEK
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+MKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKEEYDESGPSIVHRKCF
diff --git a/network/wwwblast/db/CDD/ACTIN.mtx b/network/wwwblast/db/CDD/ACTIN.mtx
new file mode 100644
index 00000000..44addbf2
--- /dev/null
+++ b/network/wwwblast/db/CDD/ACTIN.mtx
@@ -0,0 +1,385 @@
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diff --git a/network/wwwblast/db/CDD/ADF.csq b/network/wwwblast/db/CDD/ADF.csq
new file mode 100644
index 00000000..64130f4b
--- /dev/null
+++ b/network/wwwblast/db/CDD/ADF.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|ADF Actin depolymerisation factor/cofilin -like domains; Severs actin filaments and binds to actin monomers
+DESLTAFNDLKLGKKYKFILFGLNDAKTEIVVKETSTDPSYDAFLEKLPENDCLYAIYDFEYEINGNEGKRSKIVFFTWS
+PDTAPVRSKMVYASSKDALRRALNGVSTDVQGTDFSEVSYDSVLERVS
diff --git a/network/wwwblast/db/CDD/ADF.mtx b/network/wwwblast/db/CDD/ADF.mtx
new file mode 100644
index 00000000..fe6c6f73
--- /dev/null
+++ b/network/wwwblast/db/CDD/ADF.mtx
@@ -0,0 +1,142 @@
+128
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diff --git a/network/wwwblast/db/CDD/ALBUMIN.csq b/network/wwwblast/db/CDD/ALBUMIN.csq
new file mode 100644
index 00000000..73e8f60d
--- /dev/null
+++ b/network/wwwblast/db/CDD/ALBUMIN.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|ALBUMIN serum albumin
+LVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQ
+LCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKA
+TKEQLKAVMDDFAAFVEKCCKADDKETCFAEE
diff --git a/network/wwwblast/db/CDD/ALBUMIN.mtx b/network/wwwblast/db/CDD/ALBUMIN.mtx
new file mode 100644
index 00000000..58a841be
--- /dev/null
+++ b/network/wwwblast/db/CDD/ALBUMIN.mtx
@@ -0,0 +1,206 @@
+192
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diff --git a/network/wwwblast/db/CDD/ANATO.csq b/network/wwwblast/db/CDD/ANATO.csq
new file mode 100644
index 00000000..68615fe2
--- /dev/null
+++ b/network/wwwblast/db/CDD/ANATO.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ANATO Anaphylatoxin homologous domain; C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins
+CCYDGAYRNDDETCEERAARIKIGPKCVKAFKDCC
diff --git a/network/wwwblast/db/CDD/ANATO.mtx b/network/wwwblast/db/CDD/ANATO.mtx
new file mode 100644
index 00000000..f4af68f2
--- /dev/null
+++ b/network/wwwblast/db/CDD/ANATO.mtx
@@ -0,0 +1,49 @@
+35
+CCYDGAYRNDDETCEERAARIKIGPKCVKAFKDCC
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.032435e-02
+-2.989266e+00
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+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/ANK.csq b/network/wwwblast/db/CDD/ANK.csq
new file mode 100644
index 00000000..456659c1
--- /dev/null
+++ b/network/wwwblast/db/CDD/ANK.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ANK ankyrin repeats; Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structure
+DGDSFLHLAIIHEEKALTMEVIRQVKGDLAFLNF
diff --git a/network/wwwblast/db/CDD/ANK.mtx b/network/wwwblast/db/CDD/ANK.mtx
new file mode 100644
index 00000000..d2e9c2b4
--- /dev/null
+++ b/network/wwwblast/db/CDD/ANK.mtx
@@ -0,0 +1,48 @@
+34
+DGDSFLHLAIIHEEKALTMEVIRQVKGDLAFLNF
+2.700000e-01
+4.700000e-02
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diff --git a/network/wwwblast/db/CDD/ANX.csq b/network/wwwblast/db/CDD/ANX.csq
new file mode 100644
index 00000000..ee84d247
--- /dev/null
+++ b/network/wwwblast/db/CDD/ANX.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ANX Annexin repeats
+GTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLL
diff --git a/network/wwwblast/db/CDD/ANX.mtx b/network/wwwblast/db/CDD/ANX.mtx
new file mode 100644
index 00000000..cbf85df6
--- /dev/null
+++ b/network/wwwblast/db/CDD/ANX.mtx
@@ -0,0 +1,67 @@
+53
+GTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLL
+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/AP2.csq b/network/wwwblast/db/CDD/AP2.csq
new file mode 100644
index 00000000..d2038d8c
--- /dev/null
+++ b/network/wwwblast/db/CDD/AP2.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs
+HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRVNSG
diff --git a/network/wwwblast/db/CDD/AP2.mtx b/network/wwwblast/db/CDD/AP2.mtx
new file mode 100644
index 00000000..1691c673
--- /dev/null
+++ b/network/wwwblast/db/CDD/AP2.mtx
@@ -0,0 +1,79 @@
+65
+HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRVNSG
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
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+5.469651e-02
+-2.905955e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/AP2Ec.csq b/network/wwwblast/db/CDD/AP2Ec.csq
new file mode 100644
index 00000000..b5dff75d
--- /dev/null
+++ b/network/wwwblast/db/CDD/AP2Ec.csq
@@ -0,0 +1,5 @@
+>gnl|Smart|AP2Ec AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites
+YIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTE
+ALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLA
+AIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHD
+AFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKAQQ
diff --git a/network/wwwblast/db/CDD/AP2Ec.mtx b/network/wwwblast/db/CDD/AP2Ec.mtx
new file mode 100644
index 00000000..e9c63b0f
--- /dev/null
+++ b/network/wwwblast/db/CDD/AP2Ec.mtx
@@ -0,0 +1,291 @@
+277
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diff --git a/network/wwwblast/db/CDD/APPLE.csq b/network/wwwblast/db/CDD/APPLE.csq
new file mode 100644
index 00000000..df6a9509
--- /dev/null
+++ b/network/wwwblast/db/CDD/APPLE.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|APPLE APPLE domain; Four-fold repeat in plasma kallikrein and coagulation factor XI. Factor XI apple 3 mediates binding to platelets. Factor XI apple 1 binds high-molecular-mass kininogen. Apple 4 in factor XI mediates dimer formation and binds to factor XIIa. Mutations in apple 4 cause factor XI deficiency, an inherited bleeding disorder
+CMTQLYKNTFFRGGDLAAIYTPDAQYCQKMCTFHPRCLLFSFLAVTPPKETNKRFGCFMKESITGTLPRIHRTGAISGHS
+LKQC
diff --git a/network/wwwblast/db/CDD/APPLE.mtx b/network/wwwblast/db/CDD/APPLE.mtx
new file mode 100644
index 00000000..7f0198be
--- /dev/null
+++ b/network/wwwblast/db/CDD/APPLE.mtx
@@ -0,0 +1,98 @@
+84
+CMTQLYKNTFFRGGDLAAIYTPDAQYCQKMCTFHPRCLLFSFLAVTPPKETNKRFGCFMKESITGTLPRIHRTGAISGHSLKQC
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
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diff --git a/network/wwwblast/db/CDD/ARF.csq b/network/wwwblast/db/CDD/ARF.csq
new file mode 100644
index 00000000..e8df12ef
--- /dev/null
+++ b/network/wwwblast/db/CDD/ARF.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|ARF ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop)
+MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH
+YFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCA
+TSGDGLYEGLDWLSNQLRNQK
diff --git a/network/wwwblast/db/CDD/ARF.mtx b/network/wwwblast/db/CDD/ARF.mtx
new file mode 100644
index 00000000..06fb5cad
--- /dev/null
+++ b/network/wwwblast/db/CDD/ARF.mtx
@@ -0,0 +1,195 @@
+181
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+2.700000e-01
+4.700000e-02
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+1.340000e-01
+0.000000e+00
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diff --git a/network/wwwblast/db/CDD/ARM.csq b/network/wwwblast/db/CDD/ARM.csq
new file mode 100644
index 00000000..13f0c5d4
--- /dev/null
+++ b/network/wwwblast/db/CDD/ARM.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ARM Armadillo/beta-catenin-like repeats; Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin
+KEASRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSH
diff --git a/network/wwwblast/db/CDD/ARM.mtx b/network/wwwblast/db/CDD/ARM.mtx
new file mode 100644
index 00000000..aebd3eb8
--- /dev/null
+++ b/network/wwwblast/db/CDD/ARM.mtx
@@ -0,0 +1,57 @@
+43
+KEASRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSH
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
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+5.309445e-02
+-2.935683e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/AT_hook.csq b/network/wwwblast/db/CDD/AT_hook.csq
new file mode 100644
index 00000000..60ccd254
--- /dev/null
+++ b/network/wwwblast/db/CDD/AT_hook.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|AT_hook DNA binding domain with preference for A/T rich regions; Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y)
+KRPRGRPKGSKNK
diff --git a/network/wwwblast/db/CDD/AT_hook.mtx b/network/wwwblast/db/CDD/AT_hook.mtx
new file mode 100644
index 00000000..d15ee530
--- /dev/null
+++ b/network/wwwblast/db/CDD/AT_hook.mtx
@@ -0,0 +1,27 @@
+13
+KRPRGRPKGSKNK
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.682651e-02
+-2.867752e+00
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+1.340000e-01
+0.000000e+00
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+-32768  1  -32768  -4  1  0  -1  -1  0  0  2  -3  -1  0  2  0  1  1  -1  -1  -5  -1  -3  -32768  -32768  -32768  
+-32768  0  -32768  -4  0  1  -1  1  -3  -3  2  -2  -3  2  1  0  0  1  1  0  -4  -1  -3  -32768  -32768  -32768  
+-32768  1  -32768  -4  2  1  -4  0  -3  0  1  0  0  -2  1  0  -1  1  0  -2  -5  -1  -4  -32768  -32768  -32768  
diff --git a/network/wwwblast/db/CDD/AXH.csq b/network/wwwblast/db/CDD/AXH.csq
new file mode 100644
index 00000000..4dbb9d32
--- /dev/null
+++ b/network/wwwblast/db/CDD/AXH.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|AXH domain in Ataxins and HMG containing proteins; unknown function
+TVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEGCDNEEDLQMGIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVED
+GLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHP
diff --git a/network/wwwblast/db/CDD/AXH.mtx b/network/wwwblast/db/CDD/AXH.mtx
new file mode 100644
index 00000000..fe98edd4
--- /dev/null
+++ b/network/wwwblast/db/CDD/AXH.mtx
@@ -0,0 +1,145 @@
+131
+TVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEGCDNEEDLQMGIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVEDGLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHP
+2.700000e-01
+4.700000e-02
+-3.057608e+00
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+4.632298e-02
+-3.072117e+00
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+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/ArfGap.csq b/network/wwwblast/db/CDD/ArfGap.csq
new file mode 100644
index 00000000..b2a85ebb
--- /dev/null
+++ b/network/wwwblast/db/CDD/ArfGap.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs
+IGDDVSTILRGLPGNNACAECNAPEPDWASLNLGVLLCIQCSGVHRNLGVHISKVRSLSLDVKVWEPTILDLFRNLGNVY
+CNSLWEGLLHLDDDCEDGSALSHASVSKPCPEDSFSVKEKYILGKYLEKALVIKDESEA
diff --git a/network/wwwblast/db/CDD/ArfGap.mtx b/network/wwwblast/db/CDD/ArfGap.mtx
new file mode 100644
index 00000000..89934686
--- /dev/null
+++ b/network/wwwblast/db/CDD/ArfGap.mtx
@@ -0,0 +1,153 @@
+139
+IGDDVSTILRGLPGNNACAECNAPEPDWASLNLGVLLCIQCSGVHRNLGVHISKVRSLSLDVKVWEPTILDLFRNLGNVYCNSLWEGLLHLDDDCEDGSALSHASVSKPCPEDSFSVKEKYILGKYLEKALVIKDESEA
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.099353e-02
+-2.976057e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/B41.csq b/network/wwwblast/db/CDD/B41.csq
new file mode 100644
index 00000000..32be5548
--- /dev/null
+++ b/network/wwwblast/db/CDD/B41.csq
@@ -0,0 +1,5 @@
+>gnl|Smart|B41 Band 4.1 homologues; Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs
+EEKIFELLRRLPSTSNFFVFDYWTIEDNFETCCRNQLSQFTCYCNSIVSRIGDSLNFACVDNGHYRNVMFSINYLIDQKL
+FDKVVKPKTGKNIVIYKVKLLTNLNLSNKILFQFQDQVISGSLPCPKEEAAYLASIQLSVEEQWPSNKRTQTIRRHLLKG
+QFGRIRDLAQKIMVTPWEVDQNLYCTPPRFPNESANASRAQSVVEEIQHRSRTPTLLRCITNTDGLMSEEMQAQCLPVDL
+RGDRRTIKLVKERKRKLFHSQVYESEIGMKKLYIQTAKKLAAFGCKVF
diff --git a/network/wwwblast/db/CDD/B41.mtx b/network/wwwblast/db/CDD/B41.mtx
new file mode 100644
index 00000000..54474b45
--- /dev/null
+++ b/network/wwwblast/db/CDD/B41.mtx
@@ -0,0 +1,302 @@
+288
+EEKIFELLRRLPSTSNFFVFDYWTIEDNFETCCRNQLSQFTCYCNSIVSRIGDSLNFACVDNGHYRNVMFSINYLIDQKLFDKVVKPKTGKNIVIYKVKLLTNLNLSNKILFQFQDQVISGSLPCPKEEAAYLASIQLSVEEQWPSNKRTQTIRRHLLKGQFGRIRDLAQKIMVTPWEVDQNLYCTPPRFPNESANASRAQSVVEEIQHRSRTPTLLRCITNTDGLMSEEMQAQCLPVDLRGDRRTIKLVKERKRKLFHSQVYESEIGMKKLYIQTAKKLAAFGCKVF
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.040353e-02
+-2.987694e+00
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+1.340000e-01
+0.000000e+00
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diff --git a/network/wwwblast/db/CDD/BAG.csq b/network/wwwblast/db/CDD/BAG.csq
new file mode 100644
index 00000000..9e6052ad
--- /dev/null
+++ b/network/wwwblast/db/CDD/BAG.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|BAG BAG domains, present in regulator of Hsp70 proteins; BAG domains, present in Bcl-2-associated athanogene 1 and silencer of death domains
+QIDNVSLRYGNELEGRSKDLINRFDVEDEKDIYERNYCNEMLLKLLIELDSIDLINVDESLRRPLKEKRKGVIKEIQAML
+KSLDSLK
diff --git a/network/wwwblast/db/CDD/BAG.mtx b/network/wwwblast/db/CDD/BAG.mtx
new file mode 100644
index 00000000..3531e1b7
--- /dev/null
+++ b/network/wwwblast/db/CDD/BAG.mtx
@@ -0,0 +1,101 @@
+87
+QIDNVSLRYGNELEGRSKDLINRFDVEDEKDIYERNYCNEMLLKLLIELDSIDLINVDESLRRPLKEKRKGVIKEIQAMLKSLDSLK
+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/BAH.csq b/network/wwwblast/db/CDD/BAH.csq
new file mode 100644
index 00000000..836fe631
--- /dev/null
+++ b/network/wwwblast/db/CDD/BAH.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|BAH Bromo adjacent homology domain
+REMHVNSTVIYLSDSDEPSSIEYLNGDNLTQVESGSALSSGGNEGIVSLDLNNPTKSTKRKGKRVTRTAVQEQNKRSICF
+FIGEPLSCEEAQERWRWRYELKMEKATSEFSGFTEQRIQCVYKFFSFIMERQATNHDKRRLFYSTVMNDNPVDCLISKVT
+VLQVSPRVGLKPNSIKSDYYFDMEYCVEYSTFQTLR
diff --git a/network/wwwblast/db/CDD/BAH.mtx b/network/wwwblast/db/CDD/BAH.mtx
new file mode 100644
index 00000000..cf7ba8c8
--- /dev/null
+++ b/network/wwwblast/db/CDD/BAH.mtx
@@ -0,0 +1,210 @@
+196
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+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
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+4.772332e-02
+-3.042335e+00
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+0.000000e+00
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diff --git a/network/wwwblast/db/CDD/BASIC.csq b/network/wwwblast/db/CDD/BASIC.csq
new file mode 100644
index 00000000..b9cd756e
--- /dev/null
+++ b/network/wwwblast/db/CDD/BASIC.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|BASIC Basic domain in HLH proteins of MYOD family
+MELLSPPLRDIDLTGPDGSLCSFETADDFYDDPCFDSPDLRFFEDLDPRLVHVGALLKPEEHAHFSTAVHPGPGAREDEH
+VRAPSGHHQAGRCLLWACKACKRKTTNADRRKAA
diff --git a/network/wwwblast/db/CDD/BASIC.mtx b/network/wwwblast/db/CDD/BASIC.mtx
new file mode 100644
index 00000000..a9fa8a2f
--- /dev/null
+++ b/network/wwwblast/db/CDD/BASIC.mtx
@@ -0,0 +1,128 @@
+114
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diff --git a/network/wwwblast/db/CDD/BBC.csq b/network/wwwblast/db/CDD/BBC.csq
new file mode 100644
index 00000000..77a131af
--- /dev/null
+++ b/network/wwwblast/db/CDD/BBC.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|BBC B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
+IRASILDMAHCIRTFTEEISDYSRKLVGIVQHIEGGEQIVEDGIGMAHTEHVPGTAENARSCIRAYFYDLHETLCRQEEM
+ALSVVDAHVREKLIWLRQQQEDMTILLSEVSAACLHCEKTLQQDDCRVVLAKQEITRLLETLQKQ
diff --git a/network/wwwblast/db/CDD/BBC.mtx b/network/wwwblast/db/CDD/BBC.mtx
new file mode 100644
index 00000000..7b44fd91
--- /dev/null
+++ b/network/wwwblast/db/CDD/BBC.mtx
@@ -0,0 +1,159 @@
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diff --git a/network/wwwblast/db/CDD/BBOX.csq b/network/wwwblast/db/CDD/BBOX.csq
new file mode 100644
index 00000000..d57ae5ca
--- /dev/null
+++ b/network/wwwblast/db/CDD/BBOX.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BBOX B-Box-type zinc finger
+RPLEKCSEHDERLKLYCKDDGTLSCVICRDSLKHASHNFLPI
diff --git a/network/wwwblast/db/CDD/BBOX.mtx b/network/wwwblast/db/CDD/BBOX.mtx
new file mode 100644
index 00000000..10e30d07
--- /dev/null
+++ b/network/wwwblast/db/CDD/BBOX.mtx
@@ -0,0 +1,56 @@
+42
+RPLEKCSEHDERLKLYCKDDGTLSCVICRDSLKHASHNFLPI
+2.700000e-01
+4.700000e-02
+-3.057608e+00
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diff --git a/network/wwwblast/db/CDD/BCL.csq b/network/wwwblast/db/CDD/BCL.csq
new file mode 100644
index 00000000..ecf0308c
--- /dev/null
+++ b/network/wwwblast/db/CDD/BCL.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions; (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
+LREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASW
+MATYLNDHLEPWIQENGGW
diff --git a/network/wwwblast/db/CDD/BCL.mtx b/network/wwwblast/db/CDD/BCL.mtx
new file mode 100644
index 00000000..6b35c6b0
--- /dev/null
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diff --git a/network/wwwblast/db/CDD/BH4.csq b/network/wwwblast/db/CDD/BH4.csq
new file mode 100644
index 00000000..3c2bf659
--- /dev/null
+++ b/network/wwwblast/db/CDD/BH4.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BH4 BH4 Bcl-2 homology region 4
+MSQSNRELVVDFLSYKLSQKGYSWSQF
diff --git a/network/wwwblast/db/CDD/BH4.mtx b/network/wwwblast/db/CDD/BH4.mtx
new file mode 100644
index 00000000..25f66cf6
--- /dev/null
+++ b/network/wwwblast/db/CDD/BH4.mtx
@@ -0,0 +1,41 @@
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diff --git a/network/wwwblast/db/CDD/BHL.csq b/network/wwwblast/db/CDD/BHL.csq
new file mode 100644
index 00000000..d5cb2d9e
--- /dev/null
+++ b/network/wwwblast/db/CDD/BHL.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|BHL bacterial (prokaryotic) histone like domain
+MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHF
+KPGKELRDRAN
diff --git a/network/wwwblast/db/CDD/BHL.mtx b/network/wwwblast/db/CDD/BHL.mtx
new file mode 100644
index 00000000..359ea402
--- /dev/null
+++ b/network/wwwblast/db/CDD/BHL.mtx
@@ -0,0 +1,105 @@
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diff --git a/network/wwwblast/db/CDD/BIR.csq b/network/wwwblast/db/CDD/BIR.csq
new file mode 100644
index 00000000..7d64542a
--- /dev/null
+++ b/network/wwwblast/db/CDD/BIR.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BIR Baculoviral inhibition of apoptosis protein repeat; Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes
+QTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIR
diff --git a/network/wwwblast/db/CDD/BIR.mtx b/network/wwwblast/db/CDD/BIR.mtx
new file mode 100644
index 00000000..753de4ed
--- /dev/null
+++ b/network/wwwblast/db/CDD/BIR.mtx
@@ -0,0 +1,86 @@
+72
+QTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIR
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
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diff --git a/network/wwwblast/db/CDD/BPI1.csq b/network/wwwblast/db/CDD/BPI1.csq
new file mode 100644
index 00000000..0c4cfedd
--- /dev/null
+++ b/network/wwwblast/db/CDD/BPI1.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|BPI1 BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain
+RISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSSQISMVPNVGLKFSISNANIKI
+SGKWKAQKRFLKMSGNFDLSIEGMSISADLKLGSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWLIQLFHKKIESALR
+NKMNSQVCEKVTNSVSSKLQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENH
diff --git a/network/wwwblast/db/CDD/BPI1.mtx b/network/wwwblast/db/CDD/BPI1.mtx
new file mode 100644
index 00000000..4025ff36
--- /dev/null
+++ b/network/wwwblast/db/CDD/BPI1.mtx
@@ -0,0 +1,240 @@
+226
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+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/BPI2.csq b/network/wwwblast/db/CDD/BPI2.csq
new file mode 100644
index 00000000..ebf26efd
--- /dev/null
+++ b/network/wwwblast/db/CDD/BPI2.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|BPI2 BPI/LBP/CETP C-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain
+AAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESKFRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLS
+VQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNY
+IVPILVLPRVNEKLQKGFPLPTPARVQLYNVVLQPHQNFLLFGA
diff --git a/network/wwwblast/db/CDD/BPI2.mtx b/network/wwwblast/db/CDD/BPI2.mtx
new file mode 100644
index 00000000..017ae558
--- /dev/null
+++ b/network/wwwblast/db/CDD/BPI2.mtx
@@ -0,0 +1,218 @@
+204
+AAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESKFRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFPLPTPARVQLYNVVLQPHQNFLLFGA
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.669314e-02
+-2.870102e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/BRCT.csq b/network/wwwblast/db/CDD/BRCT.csq
new file mode 100644
index 00000000..7f343508
--- /dev/null
+++ b/network/wwwblast/db/CDD/BRCT.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BRCT breast cancer carboxy-terminal domain
+PDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNEKQ
diff --git a/network/wwwblast/db/CDD/BRCT.mtx b/network/wwwblast/db/CDD/BRCT.mtx
new file mode 100644
index 00000000..3f0a9a8c
--- /dev/null
+++ b/network/wwwblast/db/CDD/BRCT.mtx
@@ -0,0 +1,94 @@
+80
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diff --git a/network/wwwblast/db/CDD/BRIGHT.csq b/network/wwwblast/db/CDD/BRIGHT.csq
new file mode 100644
index 00000000..1e21ab26
--- /dev/null
+++ b/network/wwwblast/db/CDD/BRIGHT.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure
+PKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSS
diff --git a/network/wwwblast/db/CDD/BRIGHT.mtx b/network/wwwblast/db/CDD/BRIGHT.mtx
new file mode 100644
index 00000000..bda67c46
--- /dev/null
+++ b/network/wwwblast/db/CDD/BRIGHT.mtx
@@ -0,0 +1,82 @@
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diff --git a/network/wwwblast/db/CDD/BRLZ.csq b/network/wwwblast/db/CDD/BRLZ.csq
new file mode 100644
index 00000000..a7b747af
--- /dev/null
+++ b/network/wwwblast/db/CDD/BRLZ.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BRLZ basic region leucin zipper
+GRDEALRLKQRRRTLKNRGYAQACRSKRLQQRRGLEAERARLAAQLDALRAEVARLARERDLYKARCDR
diff --git a/network/wwwblast/db/CDD/BRLZ.mtx b/network/wwwblast/db/CDD/BRLZ.mtx
new file mode 100644
index 00000000..eb57aae1
--- /dev/null
+++ b/network/wwwblast/db/CDD/BRLZ.mtx
@@ -0,0 +1,83 @@
+69
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diff --git a/network/wwwblast/db/CDD/BROMO.csq b/network/wwwblast/db/CDD/BROMO.csq
new file mode 100644
index 00000000..60a86fad
--- /dev/null
+++ b/network/wwwblast/db/CDD/BROMO.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|BROMO bromo domain
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+EYNAPESEYYKCANILEKFFFSKIKEAGL
diff --git a/network/wwwblast/db/CDD/BROMO.mtx b/network/wwwblast/db/CDD/BROMO.mtx
new file mode 100644
index 00000000..89574b8c
--- /dev/null
+++ b/network/wwwblast/db/CDD/BROMO.mtx
@@ -0,0 +1,123 @@
+109
+EPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRSPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNAPESEYYKCANILEKFFFSKIKEAGL
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diff --git a/network/wwwblast/db/CDD/BTB.csq b/network/wwwblast/db/CDD/BTB.csq
new file mode 100644
index 00000000..e8f71929
--- /dev/null
+++ b/network/wwwblast/db/CDD/BTB.csq
@@ -0,0 +1,4 @@
+>gnl|Smart|BTB Broad-Complex, Tramtrack and Bric a brac; Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures
+ADVILVLQERVRIFAHKIYLSTSSSKFYDLFLMDLSEGELGGPSEPGGTHPEDHQGHSDQHHHHHHHHHGRDFLLRAASF
+DVCESVDEAGGSGPAGLRASTSDGILRGNGTGYLPGRGRVLSSWSRAFVSIQEEMAEDPLTYKSRLMVVVKMDSSIQPGP
+FRAVLKYLYTGELDENERDLMHIAHIAELLEVFDLRMMVANILNNEA
diff --git a/network/wwwblast/db/CDD/BTB.mtx b/network/wwwblast/db/CDD/BTB.mtx
new file mode 100644
index 00000000..6fef61be
--- /dev/null
+++ b/network/wwwblast/db/CDD/BTB.mtx
@@ -0,0 +1,221 @@
+207
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+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+4.699699e-02
+-3.057672e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/BTK.csq b/network/wwwblast/db/CDD/BTK.csq
new file mode 100644
index 00000000..25c945a8
--- /dev/null
+++ b/network/wwwblast/db/CDD/BTK.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BTK Bruton's tyrosine kinase Cys-rich motif; Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region
+NSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILEN
diff --git a/network/wwwblast/db/CDD/BTK.mtx b/network/wwwblast/db/CDD/BTK.mtx
new file mode 100644
index 00000000..4215e9e7
--- /dev/null
+++ b/network/wwwblast/db/CDD/BTK.mtx
@@ -0,0 +1,50 @@
+36
+NSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILEN
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.631683e-02
+-2.876762e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/B_lectin.csq b/network/wwwblast/db/CDD/B_lectin.csq
new file mode 100644
index 00000000..e0ee082e
--- /dev/null
+++ b/network/wwwblast/db/CDD/B_lectin.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|B_lectin Bulb-type mannose-specific lectin
+DNILYSGETLSTGEFLNYGSFVFIMQEDCNLVLYDVDKPIWATNTGGLSRSCFLSMQTDGNLVVYNPSNKPIWASNTGGQ
+NGNYVCILQKDRNVVIYGTDRWATGTHT
diff --git a/network/wwwblast/db/CDD/B_lectin.mtx b/network/wwwblast/db/CDD/B_lectin.mtx
new file mode 100644
index 00000000..0833bc25
--- /dev/null
+++ b/network/wwwblast/db/CDD/B_lectin.mtx
@@ -0,0 +1,122 @@
+108
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diff --git a/network/wwwblast/db/CDD/BowB.csq b/network/wwwblast/db/CDD/BowB.csq
new file mode 100644
index 00000000..03820161
--- /dev/null
+++ b/network/wwwblast/db/CDD/BowB.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|BowB Bowman-Birk type proteinase inhibitor
+CCDQCSCTKSMPPKCRCSDIRLNSCHSACKSCACTYSIPAKCFCTDINDFCYEPC
diff --git a/network/wwwblast/db/CDD/BowB.mtx b/network/wwwblast/db/CDD/BowB.mtx
new file mode 100644
index 00000000..34efef37
--- /dev/null
+++ b/network/wwwblast/db/CDD/BowB.mtx
@@ -0,0 +1,69 @@
+55
+CCDQCSCTKSMPPKCRCSDIRLNSCHSACKSCACTYSIPAKCFCTDINDFCYEPC
+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/C1.csq b/network/wwwblast/db/CDD/C1.csq
new file mode 100644
index 00000000..b80386fa
--- /dev/null
+++ b/network/wwwblast/db/CDD/C1.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains
+TTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMC
diff --git a/network/wwwblast/db/CDD/C1.mtx b/network/wwwblast/db/CDD/C1.mtx
new file mode 100644
index 00000000..a4557c5e
--- /dev/null
+++ b/network/wwwblast/db/CDD/C1.mtx
@@ -0,0 +1,62 @@
+48
+TTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMC
+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/C1Q.csq b/network/wwwblast/db/CDD/C1Q.csq
new file mode 100644
index 00000000..2a7a06aa
--- /dev/null
+++ b/network/wwwblast/db/CDD/C1Q.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|C1Q Complement component C1q domain.; Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor
+VRSGSAKVAFSAIRSTNHEPSEMSNRTMIIYFDQVLVNIGNNFDSERSTFIAPRKGIYSFNFHVVKVYNRQTIQVSLMLN
+GWPVISAFAGDQDVTREAASNGVLIQMEKGDRAYLKLERGNLMGGWKYSTFSGFLVFPL
diff --git a/network/wwwblast/db/CDD/C1Q.mtx b/network/wwwblast/db/CDD/C1Q.mtx
new file mode 100644
index 00000000..7652b3ae
--- /dev/null
+++ b/network/wwwblast/db/CDD/C1Q.mtx
@@ -0,0 +1,153 @@
+139
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diff --git a/network/wwwblast/db/CDD/C2.csq b/network/wwwblast/db/CDD/C2.csq
new file mode 100644
index 00000000..a92c7460
--- /dev/null
+++ b/network/wwwblast/db/CDD/C2.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|C2 Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles
+LLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCI
+GHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVE
diff --git a/network/wwwblast/db/CDD/C2.mtx b/network/wwwblast/db/CDD/C2.mtx
new file mode 100644
index 00000000..ebcdc9d0
--- /dev/null
+++ b/network/wwwblast/db/CDD/C2.mtx
@@ -0,0 +1,130 @@
+116
+LLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCIGHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVE
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+4.013166e-02
+-3.215590e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/C4.csq b/network/wwwblast/db/CDD/C4.csq
new file mode 100644
index 00000000..1c7778d6
--- /dev/null
+++ b/network/wwwblast/db/CDD/C4.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|C4 C-terminal tandem repeated domain in type 4 procollagens; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome
+ANVIAVHSQTIQIPNCPNGWNSLWIGYSFAMHTGAGAEGGGQSLSSPGSCLEDFRATPFIECNGARGTCHYFANKFSFWL
+TTIEDDQQFRIPESETLKAGSLRTRVSRCQVCIRS
diff --git a/network/wwwblast/db/CDD/C4.mtx b/network/wwwblast/db/CDD/C4.mtx
new file mode 100644
index 00000000..2435982e
--- /dev/null
+++ b/network/wwwblast/db/CDD/C4.mtx
@@ -0,0 +1,129 @@
+115
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diff --git a/network/wwwblast/db/CDD/CA.csq b/network/wwwblast/db/CDD/CA.csq
new file mode 100644
index 00000000..ec00451c
--- /dev/null
+++ b/network/wwwblast/db/CDD/CA.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|CA Cadherin repeats.; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium
+RIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMN
+DNRP
diff --git a/network/wwwblast/db/CDD/CA.mtx b/network/wwwblast/db/CDD/CA.mtx
new file mode 100644
index 00000000..c5d2661c
--- /dev/null
+++ b/network/wwwblast/db/CDD/CA.mtx
@@ -0,0 +1,98 @@
+84
+RIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMNDNRP
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diff --git a/network/wwwblast/db/CDD/CAD.csq b/network/wwwblast/db/CDD/CAD.csq
new file mode 100644
index 00000000..c49a3062
--- /dev/null
+++ b/network/wwwblast/db/CDD/CAD.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|CAD Domains present in proteins implicated in post-mortem DNA fragmentation
+RPFRVCDHKRTIRKGLTAATRQELLAKALETLLLNGVLTLVLEEDGTAVDSEDFFQLLEDDTCLMVLQSGQSW
diff --git a/network/wwwblast/db/CDD/CAD.mtx b/network/wwwblast/db/CDD/CAD.mtx
new file mode 100644
index 00000000..65200c50
--- /dev/null
+++ b/network/wwwblast/db/CDD/CAD.mtx
@@ -0,0 +1,87 @@
+73
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diff --git a/network/wwwblast/db/CDD/CALCITONIN.csq b/network/wwwblast/db/CDD/CALCITONIN.csq
new file mode 100644
index 00000000..daec154e
--- /dev/null
+++ b/network/wwwblast/db/CDD/CALCITONIN.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|CALCITONIN calcitonin; This family is formed by calcitonin, the calcitonin gene-related peptide, and amylin. They are short polypeptide hormones
+KRACNTATCVTHRLADFLSRSGGVGKNNFVPTNVGSKAFGRRR
diff --git a/network/wwwblast/db/CDD/CALCITONIN.mtx b/network/wwwblast/db/CDD/CALCITONIN.mtx
new file mode 100644
index 00000000..37eada0d
--- /dev/null
+++ b/network/wwwblast/db/CDD/CALCITONIN.mtx
@@ -0,0 +1,57 @@
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diff --git a/network/wwwblast/db/CDD/CARD.csq b/network/wwwblast/db/CDD/CARD.csq
new file mode 100644
index 00000000..148c6a84
--- /dev/null
+++ b/network/wwwblast/db/CDD/CARD.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|CARD Caspase recruitment domain; Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain
+MDEADRRLLRRCRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDT
+GQDMLASFLRT
diff --git a/network/wwwblast/db/CDD/CARD.mtx b/network/wwwblast/db/CDD/CARD.mtx
new file mode 100644
index 00000000..a0777a91
--- /dev/null
+++ b/network/wwwblast/db/CDD/CARD.mtx
@@ -0,0 +1,105 @@
+91
+MDEADRRLLRRCRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRT
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.469011e-02
+-2.906072e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/CASc.csq b/network/wwwblast/db/CDD/CASc.csq
new file mode 100644
index 00000000..d329d34c
--- /dev/null
+++ b/network/wwwblast/db/CDD/CASc.csq
@@ -0,0 +1,5 @@
+>gnl|Smart|CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues
+SYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFV
+CVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVDADFLY
+AYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYF
+YH
diff --git a/network/wwwblast/db/CDD/CASc.mtx b/network/wwwblast/db/CDD/CASc.mtx
new file mode 100644
index 00000000..30ebcd2f
--- /dev/null
+++ b/network/wwwblast/db/CDD/CASc.mtx
@@ -0,0 +1,256 @@
+242
+SYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFVCVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVDADFLYAYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYFYH
+2.700000e-01
+4.700000e-02
+-3.057608e+00
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+-2.858338e+00
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diff --git a/network/wwwblast/db/CDD/CBF.csq b/network/wwwblast/db/CDD/CBF.csq
new file mode 100644
index 00000000..9ec14ef1
--- /dev/null
+++ b/network/wwwblast/db/CDD/CBF.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|CBF CCAAT-Binding transcription Factor
+TEDSTIYVNSKQYHGIIRRRQSRAKAAAVLDQKKLSSRCRKPYMHHSRHLHALRRPRGSGGRFLNT
diff --git a/network/wwwblast/db/CDD/CBF.mtx b/network/wwwblast/db/CDD/CBF.mtx
new file mode 100644
index 00000000..b7f26402
--- /dev/null
+++ b/network/wwwblast/db/CDD/CBF.mtx
@@ -0,0 +1,80 @@
+66
+TEDSTIYVNSKQYHGIIRRRQSRAKAAAVLDQKKLSSRCRKPYMHHSRHLHALRRPRGSGGRFLNT
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diff --git a/network/wwwblast/db/CDD/CBS.csq b/network/wwwblast/db/CDD/CBS.csq
new file mode 100644
index 00000000..22367523
--- /dev/null
+++ b/network/wwwblast/db/CDD/CBS.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|CBS Domain in cystathionine beta-synthase and other proteins.; Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease
+DLVVAPAGITLKEANEILQRSKKGKLPIVNEDDELVAIIARTDLKKNRD
diff --git a/network/wwwblast/db/CDD/CBS.mtx b/network/wwwblast/db/CDD/CBS.mtx
new file mode 100644
index 00000000..790c5856
--- /dev/null
+++ b/network/wwwblast/db/CDD/CBS.mtx
@@ -0,0 +1,63 @@
+49
+DLVVAPAGITLKEANEILQRSKKGKLPIVNEDDELVAIIARTDLKKNRD
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diff --git a/network/wwwblast/db/CDD/CCP.csq b/network/wwwblast/db/CDD/CCP.csq
new file mode 100644
index 00000000..f8bb3ef0
--- /dev/null
+++ b/network/wwwblast/db/CDD/CCP.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|CCP Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII
+CEEPPTFEAMELIGKPKPYYEIGERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDAC
diff --git a/network/wwwblast/db/CDD/CCP.mtx b/network/wwwblast/db/CDD/CCP.mtx
new file mode 100644
index 00000000..eda49ea0
--- /dev/null
+++ b/network/wwwblast/db/CDD/CCP.mtx
@@ -0,0 +1,74 @@
+60
+CEEPPTFEAMELIGKPKPYYEIGERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDAC
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
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+3.372790e-02
+-3.389430e+00
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diff --git a/network/wwwblast/db/CDD/CH.csq b/network/wwwblast/db/CDD/CH.csq
new file mode 100644
index 00000000..bac491ea
--- /dev/null
+++ b/network/wwwblast/db/CDD/CH.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|CH Calponin homology domain; Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p
+EKYAFVNWINKALENDPDCRHVIPMNPNTDDLFKAVGDGIVLCKMINLSVPDTIDERAINKKKLTPFIIQENLNLALNSA
+SAIGCHVVNIGAEDLRAGKPHLVLGLLWQIIKI
diff --git a/network/wwwblast/db/CDD/CH.mtx b/network/wwwblast/db/CDD/CH.mtx
new file mode 100644
index 00000000..9d1f5568
--- /dev/null
+++ b/network/wwwblast/db/CDD/CH.mtx
@@ -0,0 +1,127 @@
+113
+EKYAFVNWINKALENDPDCRHVIPMNPNTDDLFKAVGDGIVLCKMINLSVPDTIDERAINKKKLTPFIIQENLNLALNSASAIGCHVVNIGAEDLRAGKPHLVLGLLWQIIKI
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.013248e-02
+-2.993086e+00
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+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/CHROMO.csq b/network/wwwblast/db/CDD/CHROMO.csq
new file mode 100644
index 00000000..f99808a0
--- /dev/null
+++ b/network/wwwblast/db/CDD/CHROMO.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|CHROMO Chromatin organization modifier domain
+GLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEER
diff --git a/network/wwwblast/db/CDD/CHROMO.mtx b/network/wwwblast/db/CDD/CHROMO.mtx
new file mode 100644
index 00000000..e9a44eed
--- /dev/null
+++ b/network/wwwblast/db/CDD/CHROMO.mtx
@@ -0,0 +1,66 @@
+52
+GLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEER
+2.700000e-01
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diff --git a/network/wwwblast/db/CDD/Calx_beta.csq b/network/wwwblast/db/CDD/Calx_beta.csq
new file mode 100644
index 00000000..5a3f2cf4
--- /dev/null
+++ b/network/wwwblast/db/CDD/Calx_beta.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|Calx_beta Domains in Na-Ca exchangers and integrin-beta4; Domain in Na-Ca exchangers and integrin subunit beta4 (and some cyanobacterial proteins)
+VNITIIKEQASGIVSFEQPEYSVSRGDQVARIPVIRHILDNGKSQVSYSTQDNTAHGHRDYVPVEGELLFYPGETWKELQ
+VKLLELQEVDSLLRGRQVRRFQVQLS
diff --git a/network/wwwblast/db/CDD/Calx_beta.mtx b/network/wwwblast/db/CDD/Calx_beta.mtx
new file mode 100644
index 00000000..84c9a29c
--- /dev/null
+++ b/network/wwwblast/db/CDD/Calx_beta.mtx
@@ -0,0 +1,120 @@
+106
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diff --git a/network/wwwblast/db/CDD/ChSh.csq b/network/wwwblast/db/CDD/ChSh.csq
new file mode 100644
index 00000000..271b5853
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChSh.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ChSh Chromo Shadow Domain
+RGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWH
diff --git a/network/wwwblast/db/CDD/ChSh.mtx b/network/wwwblast/db/CDD/ChSh.mtx
new file mode 100644
index 00000000..714bcda6
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChSh.mtx
@@ -0,0 +1,75 @@
+61
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diff --git a/network/wwwblast/db/CDD/CheW.csq b/network/wwwblast/db/CDD/CheW.csq
new file mode 100644
index 00000000..075658c8
--- /dev/null
+++ b/network/wwwblast/db/CDD/CheW.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|CheW Two component signalling adaptor domain
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+VIVRVGNRKYGIVVDDLLGQDDIVIKSLGKVFSEVKEFSGAAILGDGSIALIINVSGIV
diff --git a/network/wwwblast/db/CDD/CheW.mtx b/network/wwwblast/db/CDD/CheW.mtx
new file mode 100644
index 00000000..89cb9f78
--- /dev/null
+++ b/network/wwwblast/db/CDD/CheW.mtx
@@ -0,0 +1,153 @@
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diff --git a/network/wwwblast/db/CDD/ChtBD1.csq b/network/wwwblast/db/CDD/ChtBD1.csq
new file mode 100644
index 00000000..5e0450fc
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChtBD1.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ChtBD1 Chitin binding domain
+PCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC
diff --git a/network/wwwblast/db/CDD/ChtBD1.mtx b/network/wwwblast/db/CDD/ChtBD1.mtx
new file mode 100644
index 00000000..4cd18473
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChtBD1.mtx
@@ -0,0 +1,53 @@
+39
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diff --git a/network/wwwblast/db/CDD/ChtBD2.csq b/network/wwwblast/db/CDD/ChtBD2.csq
new file mode 100644
index 00000000..b109062e
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChtBD2.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ChtBD2 Chitin-binding domain type 2
+EICAPFHNGTINGRDRFPLRNCRYFAFCDTERPYLTLTQCPFNDLFNEATKTCEMHVNCGN
diff --git a/network/wwwblast/db/CDD/ChtBD2.mtx b/network/wwwblast/db/CDD/ChtBD2.mtx
new file mode 100644
index 00000000..7e2ce490
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChtBD2.mtx
@@ -0,0 +1,75 @@
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diff --git a/network/wwwblast/db/CDD/ChtBD3.csq b/network/wwwblast/db/CDD/ChtBD3.csq
new file mode 100644
index 00000000..8cf0310a
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChtBD3.csq
@@ -0,0 +1,2 @@
+>gnl|Smart|ChtBD3 Chitin-binding domain type 3
+SKDWAGGQPTHNEAGQSIVYKGNLYTANWYTASVPGSDSSWTQV
diff --git a/network/wwwblast/db/CDD/ChtBD3.mtx b/network/wwwblast/db/CDD/ChtBD3.mtx
new file mode 100644
index 00000000..33b785f5
--- /dev/null
+++ b/network/wwwblast/db/CDD/ChtBD3.mtx
@@ -0,0 +1,58 @@
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+-32768  1  -32768  -4  1  -2  -5  5  -4  -4  -3  -3  -4  1  -4  -3  -2  1  1  0  -5  -1  -5  -32768  -32768  -32768  
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+-32768  1  -32768  -5  2  -3  -5  3  -4  -5  -2  -3  -4  1  -1  2  1  1  0  -4  4  -1  -4  -32768  -32768  -32768  
+-32768  0  -32768  2  -1  -2  0  -2  -4  -2  -4  1  -3  -4  4  -1  -4  1  -1  1  -4  -1  3  -32768  -32768  -32768  
+-32768  -5  -32768  1  -6  -6  -1  -5  -4  -5  -6  -5  -4  -6  -2  -5  -6  -5  -5  -5  13  -1  3  -32768  -32768  -32768  
+-32768  -2  -32768  -5  -1  2  -5  -2  -3  -1  3  0  0  -3  -4  4  1  -1  2  -1  -5  -1  -4  -32768  -32768  -32768  
+-32768  -1  -32768  -5  2  2  -4  -4  -3  -2  1  1  -3  2  2  -1  -1  1  0  -3  -5  -1  2  -32768  -32768  -32768  
+-32768  0  -32768  2  0  -1  -3  -2  -4  2  -1  2  -2  -1  -1  1  -4  -3  -2  4  -5  -1  1  -32768  -32768  -32768  
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/14_3_3.chk b/network/wwwblast/db/CDD/Sun5.7_chk/14_3_3.chk
new file mode 100644
index 00000000..b125a64a
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/14_3_3.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/35EXOc.chk b/network/wwwblast/db/CDD/Sun5.7_chk/35EXOc.chk
new file mode 100644
index 00000000..ff0e26f5
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/35EXOc.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/4.1m.chk b/network/wwwblast/db/CDD/Sun5.7_chk/4.1m.chk
new file mode 100644
index 00000000..9ecf3053
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/4.1m.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/53EXOc.chk b/network/wwwblast/db/CDD/Sun5.7_chk/53EXOc.chk
new file mode 100644
index 00000000..8c372f8d
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/53EXOc.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/A1pp.chk b/network/wwwblast/db/CDD/Sun5.7_chk/A1pp.chk
new file mode 100644
index 00000000..58d664a4
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/A1pp.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/A4_EXTRA.chk b/network/wwwblast/db/CDD/Sun5.7_chk/A4_EXTRA.chk
new file mode 100644
index 00000000..8d2ef626
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/A4_EXTRA.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/AAA.chk b/network/wwwblast/db/CDD/Sun5.7_chk/AAA.chk
new file mode 100644
index 00000000..c675457e
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/AAA.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/AAI.chk b/network/wwwblast/db/CDD/Sun5.7_chk/AAI.chk
new file mode 100644
index 00000000..9011d917
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/AAI.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ACTIN.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ACTIN.chk
new file mode 100644
index 00000000..7239b413
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ACTIN.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ADF.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ADF.chk
new file mode 100644
index 00000000..7114639a
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ADF.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ALBUMIN.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ALBUMIN.chk
new file mode 100644
index 00000000..762044d9
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ALBUMIN.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ANATO.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ANATO.chk
new file mode 100644
index 00000000..7c6f679d
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ANATO.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ANK.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ANK.chk
new file mode 100644
index 00000000..dbd7bc2d
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ANK.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ANX.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ANX.chk
new file mode 100644
index 00000000..ff99131b
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ANX.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/AP2.chk b/network/wwwblast/db/CDD/Sun5.7_chk/AP2.chk
new file mode 100644
index 00000000..362868d2
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/AP2.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/AP2Ec.chk b/network/wwwblast/db/CDD/Sun5.7_chk/AP2Ec.chk
new file mode 100644
index 00000000..d3ed0063
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/AP2Ec.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/APPLE.chk b/network/wwwblast/db/CDD/Sun5.7_chk/APPLE.chk
new file mode 100644
index 00000000..feb9f9d0
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/APPLE.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ARF.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ARF.chk
new file mode 100644
index 00000000..7b352f40
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ARF.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ARM.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ARM.chk
new file mode 100644
index 00000000..6d38c9a1
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ARM.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/AT_hook.chk b/network/wwwblast/db/CDD/Sun5.7_chk/AT_hook.chk
new file mode 100644
index 00000000..c0b66301
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/AT_hook.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/AXH.chk b/network/wwwblast/db/CDD/Sun5.7_chk/AXH.chk
new file mode 100644
index 00000000..bff3d518
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/AXH.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ArfGap.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ArfGap.chk
new file mode 100644
index 00000000..a86c050a
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ArfGap.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/B41.chk b/network/wwwblast/db/CDD/Sun5.7_chk/B41.chk
new file mode 100644
index 00000000..69cdcd96
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/B41.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BAG.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BAG.chk
new file mode 100644
index 00000000..93f951d6
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BAG.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BAH.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BAH.chk
new file mode 100644
index 00000000..ea6da5ea
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BAH.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BASIC.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BASIC.chk
new file mode 100644
index 00000000..ca4356f2
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BASIC.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BBC.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BBC.chk
new file mode 100644
index 00000000..25ed01ea
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BBC.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BBOX.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BBOX.chk
new file mode 100644
index 00000000..ff7e9502
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BBOX.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BCL.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BCL.chk
new file mode 100644
index 00000000..75486637
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BCL.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BH4.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BH4.chk
new file mode 100644
index 00000000..e3f76b16
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BH4.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BHL.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BHL.chk
new file mode 100644
index 00000000..68730217
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BHL.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BIR.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BIR.chk
new file mode 100644
index 00000000..c3d32d14
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BIR.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BPI1.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BPI1.chk
new file mode 100644
index 00000000..7007be03
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BPI1.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BPI2.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BPI2.chk
new file mode 100644
index 00000000..dc976359
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BPI2.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BRCT.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BRCT.chk
new file mode 100644
index 00000000..7f86c2b8
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BRCT.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BRIGHT.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BRIGHT.chk
new file mode 100644
index 00000000..bd18eaca
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BRIGHT.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BRLZ.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BRLZ.chk
new file mode 100644
index 00000000..76f55607
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BRLZ.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BROMO.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BROMO.chk
new file mode 100644
index 00000000..1fca7238
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BROMO.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BTB.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BTB.chk
new file mode 100644
index 00000000..223304c6
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BTB.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BTK.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BTK.chk
new file mode 100644
index 00000000..f122950b
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BTK.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/B_lectin.chk b/network/wwwblast/db/CDD/Sun5.7_chk/B_lectin.chk
new file mode 100644
index 00000000..e6223172
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/B_lectin.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/BowB.chk b/network/wwwblast/db/CDD/Sun5.7_chk/BowB.chk
new file mode 100644
index 00000000..53eb45ba
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/BowB.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/C1.chk b/network/wwwblast/db/CDD/Sun5.7_chk/C1.chk
new file mode 100644
index 00000000..0e77c4fa
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/C1.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/C1Q.chk b/network/wwwblast/db/CDD/Sun5.7_chk/C1Q.chk
new file mode 100644
index 00000000..92f4e617
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/C1Q.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/C2.chk b/network/wwwblast/db/CDD/Sun5.7_chk/C2.chk
new file mode 100644
index 00000000..3859d90b
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/C2.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/C4.chk b/network/wwwblast/db/CDD/Sun5.7_chk/C4.chk
new file mode 100644
index 00000000..2bbc7874
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/C4.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CA.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CA.chk
new file mode 100644
index 00000000..41251a77
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CA.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CAD.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CAD.chk
new file mode 100644
index 00000000..47aaa61f
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CAD.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CALCITONIN.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CALCITONIN.chk
new file mode 100644
index 00000000..8ea1efb5
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CALCITONIN.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CARD.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CARD.chk
new file mode 100644
index 00000000..81af93ed
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CARD.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CASc.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CASc.chk
new file mode 100644
index 00000000..aefd34c7
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CASc.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CBF.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CBF.chk
new file mode 100644
index 00000000..8d09ed44
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CBF.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CBS.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CBS.chk
new file mode 100644
index 00000000..99de7076
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CBS.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CCP.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CCP.chk
new file mode 100644
index 00000000..8ff62ad6
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CCP.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CH.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CH.chk
new file mode 100644
index 00000000..3e340421
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CH.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CHROMO.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CHROMO.chk
new file mode 100644
index 00000000..69430d97
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CHROMO.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/Calx_beta.chk b/network/wwwblast/db/CDD/Sun5.7_chk/Calx_beta.chk
new file mode 100644
index 00000000..3ed03506
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/Calx_beta.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ChSh.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ChSh.chk
new file mode 100644
index 00000000..fb0d4a02
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ChSh.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/CheW.chk b/network/wwwblast/db/CDD/Sun5.7_chk/CheW.chk
new file mode 100644
index 00000000..7d6e9747
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/CheW.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD1.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD1.chk
new file mode 100644
index 00000000..d898f3dc
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD1.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD2.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD2.chk
new file mode 100644
index 00000000..9145d0cd
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD2.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD3.chk b/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD3.chk
new file mode 100644
index 00000000..8434adc4
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/ChtBD3.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/acidPPc.chk b/network/wwwblast/db/CDD/Sun5.7_chk/acidPPc.chk
new file mode 100644
index 00000000..a9f92870
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/acidPPc.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/alkPPc.chk b/network/wwwblast/db/CDD/Sun5.7_chk/alkPPc.chk
new file mode 100644
index 00000000..fb37a80f
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/alkPPc.chk
diff --git a/network/wwwblast/db/CDD/Sun5.7_chk/btg1.chk b/network/wwwblast/db/CDD/Sun5.7_chk/btg1.chk
new file mode 100644
index 00000000..fa5789dd
--- /dev/null
+++ b/network/wwwblast/db/CDD/Sun5.7_chk/btg1.chk
diff --git a/network/wwwblast/db/CDD/acidPPc.csq b/network/wwwblast/db/CDD/acidPPc.csq
new file mode 100644
index 00000000..31c634cc
--- /dev/null
+++ b/network/wwwblast/db/CDD/acidPPc.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|acidPPc Acid phosphatase homologues
+LGVIVMGISVIATQAAKTGAKALFEEPRPFTVYLAEQTHSTPENFYKNDRTLRAEIAKNFYSMDAITPAWLVHHYENETG
+YSFPSGHTIFAATWLMLAVGFTQLLGNRSFKAKLLVVGIAVWGLLMLISRVRLGMHYPIDLLVATLLAWLINSIIF
diff --git a/network/wwwblast/db/CDD/acidPPc.mtx b/network/wwwblast/db/CDD/acidPPc.mtx
new file mode 100644
index 00000000..413978a8
--- /dev/null
+++ b/network/wwwblast/db/CDD/acidPPc.mtx
@@ -0,0 +1,170 @@
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diff --git a/network/wwwblast/db/CDD/alkPPc.csq b/network/wwwblast/db/CDD/alkPPc.csq
new file mode 100644
index 00000000..723540a8
--- /dev/null
+++ b/network/wwwblast/db/CDD/alkPPc.csq
@@ -0,0 +1,7 @@
+>gnl|Smart|alkPPc Alkaline phosphatase homologues
+KNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDGAASATAWSTGVKTYNGALGV
+DIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADV
+TLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKP
+AVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNT
+LVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTM
+KAALGLK
diff --git a/network/wwwblast/db/CDD/alkPPc.mtx b/network/wwwblast/db/CDD/alkPPc.mtx
new file mode 100644
index 00000000..fd861629
--- /dev/null
+++ b/network/wwwblast/db/CDD/alkPPc.mtx
@@ -0,0 +1,421 @@
+407
+KNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDGAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK
+2.700000e-01
+4.700000e-02
+-3.057608e+00
+2.300000e-01
+2.700000e-01
+5.434204e-02
+-2.912457e+00
+2.300000e-01
+3.176000e-01
+1.340000e-01
+0.000000e+00
+4.000000e-01
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diff --git a/network/wwwblast/db/CDD/btg1.csq b/network/wwwblast/db/CDD/btg1.csq
new file mode 100644
index 00000000..62c83adc
--- /dev/null
+++ b/network/wwwblast/db/CDD/btg1.csq
@@ -0,0 +1,3 @@
+>gnl|Smart|btg1 tob/btg1 family; The tob/btg1 is a family of proteins that inhibit cell proliferation
+MKEEIAATVVFLTMLVKKHKQLSKQKIEKFAAKLTTILFAKYKNHWYAENPMKGQAFRCIRINTYQAIDAVFEKACAESN
+VDFNDLGLPKEMTIWVDPFEVCCRYGEK
diff --git a/network/wwwblast/db/CDD/btg1.mtx b/network/wwwblast/db/CDD/btg1.mtx
new file mode 100644
index 00000000..d21875cf
--- /dev/null
+++ b/network/wwwblast/db/CDD/btg1.mtx
@@ -0,0 +1,122 @@
+108
+MKEEIAATVVFLTMLVKKHKQLSKQKIEKFAAKLTTILFAKYKNHWYAENPMKGQAFRCIRINTYQAIDAVFEKACAESNVDFNDLGLPKEMTIWVDPFEVCCRYGEK
+2.700000e-01
+4.700000e-02
+-3.057608e+00
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+-3.052713e+00
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diff --git a/network/wwwblast/db/CDD/make_cdd.csh b/network/wwwblast/db/CDD/make_cdd.csh
new file mode 100755
index 00000000..753078c9
--- /dev/null
+++ b/network/wwwblast/db/CDD/make_cdd.csh
@@ -0,0 +1,12 @@
+#!/bin/csh -f
+
+#
+# First regular BLAST database should be creeated for the given concatenated list
+# of profiles in order
+#
+formatdb -i test_CDD_db -p T 
+#
+# Now we have to prepare memory-mapped lookup table and PSI matrix for collection of
+# profiles
+#
+copymat -P test_CDD_db -r T
diff --git a/network/wwwblast/db/CDD/rpsfdb.csh b/network/wwwblast/db/CDD/rpsfdb.csh
new file mode 100755
index 00000000..cd49528f
--- /dev/null
+++ b/network/wwwblast/db/CDD/rpsfdb.csh
@@ -0,0 +1,17 @@
+#!/bin/csh -f
+#
+# $Id: rpsfdb.csh,v 1.1 2002/08/06 19:04:05 dondosha Exp $
+#
+# Script for creating BLAST database from Impala *.sn file
+# Author: Sergei Shavirin
+#
+# Usage: rpsfdb.csh <name.sn>
+#
+# Suffix "sn" will be striped from input filename. All files will
+# be copied into file without suffix and BLAST database will be created 
+# with this name
+#
+set Bname = `echo $1 | awk -F. '{print $1}'`
+#
+cat `cat $1` > $Bname
+formatdb -i $Bname
diff --git a/network/wwwblast/db/CDD/test_CDD_db b/network/wwwblast/db/CDD/test_CDD_db
new file mode 100644
index 00000000..ec960602
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db
@@ -0,0 +1,197 @@
+>gnl|Smart|14_3_3 14-3-3 homologues; 14-3-3 homologues mediates signal transduction by binding to phosphoserine-containing proteins. They are involved in growth factor signalling and also interact with MEK kinases
+RDEYVYKAKLAEQAERYDEMAEAMKNLVENCLDEQQPKDELSVEERNLLSVAYKNAVGARRASWRIISSVEQKELSKQHM
+QNKALAAEYRQKVEEELNKICHDILQLLTDKLIPKTSDSESKVFYYKMKGDYYRYISEFSGEEGKKQAADQAQESYQKAT
+ETAEGHSPATHPIRLGLALNYSVFFYEILNLPQQACEMAKRAFDDAITEFDNVSEDSYKDSTLIMQLLRDNLTLWTSDLQ
+ADQQQQEGG
+>gnl|Smart|35EXOc 3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
+YVTILDEETLKAWIAKLEKAPVFAFDTETDSLDNISANLVGLSFAIEPGVAAYIPVAHDYLDAPDQISRERALELLKPLL
+EDEKALKVGQNLKYDRGILANYGIELRGIAFDTMLESYILNSVAGRHDMDSLAERWLKHKTITFEEIAGKGKNQLTFNQI
+ALEEAGRYAAEDADVTLQLHLKMWPDLQ
+>gnl|Smart|4.1m putative band 4.1 homologues' binding motif
+MYKYRNRDEGSYHVDESRN
+>gnl|Smart|53EXOc 5'-3' exonuclease
+RNLMIVDGTNLGFRFKHNNSKKPFASSYVSTIQSLAKSYSARTTIVLGDKGKSVFRLEHLPEYKGNRDEKYAQRTEEEKA
+LDEQFFEYLKDAFELCKTTFPTFTIRGVEADDMAAYIVKLIGHLYDHVWLISTDGDWDTLLTDKVSRFSFTTRREYHLRD
+MYEHHNVDDVEQFISLKAIMGDLGDNIRGVEGIGAKRGYNIIREFGNVLDIIDQLPLPGKQKYIQNLNASEELLFRNLIL
+VDLPTYCVDAIAAVG
+>gnl|Smart|A1pp Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson & Fuji)
+RFHCFKGHFSHDKILNKKSGAVVISSHSSMDFSTTLGRAFAVTTCLQRSCWEKIKNNIPTPEKHLPIGSCVSGPWDVEEG
+AQLYTSHLIVINPPTLETLIKEKMRRAITLKDFSMKEAFTNLVLAYLQCFDICIEHNLESVQLEVFGLNNLSADQEEFTT
+WE
+>gnl|Smart|A4_EXTRA amyloid A4; amyloid A4 precursor of Alzheimers disease
+QAASPRWEPQIAVLCEAGQIYQPQYLSEEGRWVTDLSKKTTGPTCLRDKMDLLDYCKKAYPNRDITNIVESSHYQKIGGW
+CRQGALNAAKCKGSHRWIKPFRCLGPFQSDALLVPEGCLFDHIHNASRCWPFVRWNQTGAAACQERGMQMRTFAMLLPCG
+ISVFSGVEFVCCP
+>gnl|Smart|AAA ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment
+TPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDAAVKMVRVQAIEKNRYRAEELAE
+ERILDVLIPPAKNNWGQTEQQQEPSAARQAFRKKLREGQLDDKEIEIDLAAAPMGVEIMAPPGMEEMTSQLQSMFQNLGG
+QKQKARKLKIKDAMKLLIEEEAAKLVNPEELKQDAIDAVEQHGIVFIDEIDKICKRGESSGPDVSREGVQRDLLPLVEGC
+TVSTKHGMVKTDHILFIASGAFQIAKPSDLIPELQGRLPIRVEL
+>gnl|Smart|AAI Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family
+CYPGQAFQVPALPACRPLLRLQCNGSQVPEAVLRDCCQQLAHISEWCRCGALYSMLDSMYKEHGAQEGQAGTGAFPRCRR
+EVVKLTAASITAVCRLPIVVDASGDGAYVC
+>gnl|Smart|acidPPc Acid phosphatase homologues
+LGVIVMGISVIATQAAKTGAKALFEEPRPFTVYLAEQTHSTPENFYKNDRTLRAEIAKNFYSMDAITPAWLVHHYENETG
+YSFPSGHTIFAATWLMLAVGFTQLLGNRSFKAKLLVVGIAVWGLLMLISRVRLGMHYPIDLLVATLLAWLINSIIF
+>gnl|Smart|ACTIN Actin; ACTIN subfamily of ACTIN/mreB/sugarkinase/Hsp70 superfamily
+VQALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEK
+IWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVSHTVP
+IYEGYALPHAILRLDLAGRDLTDYMMKILTERGYSFTTTAEREIVRDIKEKLAYVALDFEQEMATAASSSALEKSYELPD
+GQVITIGNERFRCPEALFQPSFLGMESAGIHETTYNSIMKCDVDIRKDLYGNVVLSGGTTMFPGIADRMNKELTALAPST
+MKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKEEYDESGPSIVHRKCF
+>gnl|Smart|ADF Actin depolymerisation factor/cofilin -like domains; Severs actin filaments and binds to actin monomers
+DESLTAFNDLKLGKKYKFILFGLNDAKTEIVVKETSTDPSYDAFLEKLPENDCLYAIYDFEYEINGNEGKRSKIVFFTWS
+PDTAPVRSKMVYASSKDALRRALNGVSTDVQGTDFSEVSYDSVLERVS
+>gnl|Smart|ALBUMIN serum albumin
+LVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQ
+LCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKA
+TKEQLKAVMDDFAAFVEKCCKADDKETCFAEE
+>gnl|Smart|alkPPc Alkaline phosphatase homologues
+KNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDGAASATAWSTGVKTYNGALGV
+DIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADV
+TLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKP
+AVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNT
+LVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTM
+KAALGLK
+>gnl|Smart|ANATO Anaphylatoxin homologous domain; C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins
+CCYDGAYRNDDETCEERAARIKIGPKCVKAFKDCC
+>gnl|Smart|ANK ankyrin repeats; Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structure
+DGDSFLHLAIIHEEKALTMEVIRQVKGDLAFLNF
+>gnl|Smart|ANX Annexin repeats
+GTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLL
+>gnl|Smart|AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs
+HYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRVNSG
+>gnl|Smart|AP2Ec AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites
+YIGAHVSAAGGLANAAIRAAEIDATAFALFTKNQRQWRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTE
+ALEKSRDAFIDEMQRCEQLGLSLLNFHPGSHLMQISEEDCLARIAESINIALDKTQGVTAVIENTAGQGSNLGFKFEHLA
+AIIDGVEDKSRVGVCIDTCHAFAAGYDLRTPAECEKTFADFARTVGFKYLRGMHLNDAKSTFGSRVDRHHSLGEGNIGHD
+AFRWIMQDDRFDGIPLILETINPDIWAEEIAWLKAQQ
+>gnl|Smart|APPLE APPLE domain; Four-fold repeat in plasma kallikrein and coagulation factor XI. Factor XI apple 3 mediates binding to platelets. Factor XI apple 1 binds high-molecular-mass kininogen. Apple 4 in factor XI mediates dimer formation and binds to factor XIIa. Mutations in apple 4 cause factor XI deficiency, an inherited bleeding disorder
+CMTQLYKNTFFRGGDLAAIYTPDAQYCQKMCTFHPRCLLFSFLAVTPPKETNKRFGCFMKESITGTLPRIHRTGAISGHS
+LKQC
+>gnl|Smart|ARF ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop)
+MGNIFANLFKGLFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRH
+YFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCA
+TSGDGLYEGLDWLSNQLRNQK
+>gnl|Smart|ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs
+IGDDVSTILRGLPGNNACAECNAPEPDWASLNLGVLLCIQCSGVHRNLGVHISKVRSLSLDVKVWEPTILDLFRNLGNVY
+CNSLWEGLLHLDDDCEDGSALSHASVSKPCPEDSFSVKEKYILGKYLEKALVIKDESEA
+>gnl|Smart|ARM Armadillo/beta-catenin-like repeats; Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin
+KEASRHAIMRSPQMVSAIVRTMQNTNDVETARCTAGTLHNLSH
+>gnl|Smart|AT_hook DNA binding domain with preference for A/T rich regions; Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y)
+KRPRGRPKGSKNK
+>gnl|Smart|AXH domain in Ataxins and HMG containing proteins; unknown function
+TVWHCFLKGTRLCFHKGSNKEWQDVEDFARAEGCDNEEDLQMGIHKGYGSDGLKLLSHEESVSFGESVLKLTFDPGTVED
+GLLTVECKLDHPFYVKNKGWSSFYPSLTVVQHGIPCCEVHIGDVCLPPGHP
+>gnl|Smart|B41 Band 4.1 homologues; Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs
+EEKIFELLRRLPSTSNFFVFDYWTIEDNFETCCRNQLSQFTCYCNSIVSRIGDSLNFACVDNGHYRNVMFSINYLIDQKL
+FDKVVKPKTGKNIVIYKVKLLTNLNLSNKILFQFQDQVISGSLPCPKEEAAYLASIQLSVEEQWPSNKRTQTIRRHLLKG
+QFGRIRDLAQKIMVTPWEVDQNLYCTPPRFPNESANASRAQSVVEEIQHRSRTPTLLRCITNTDGLMSEEMQAQCLPVDL
+RGDRRTIKLVKERKRKLFHSQVYESEIGMKKLYIQTAKKLAAFGCKVF
+>gnl|Smart|B_lectin Bulb-type mannose-specific lectin
+DNILYSGETLSTGEFLNYGSFVFIMQEDCNLVLYDVDKPIWATNTGGLSRSCFLSMQTDGNLVVYNPSNKPIWASNTGGQ
+NGNYVCILQKDRNVVIYGTDRWATGTHT
+>gnl|Smart|BAG BAG domains, present in regulator of Hsp70 proteins; BAG domains, present in Bcl-2-associated athanogene 1 and silencer of death domains
+QIDNVSLRYGNELEGRSKDLINRFDVEDEKDIYERNYCNEMLLKLLIELDSIDLINVDESLRRPLKEKRKGVIKEIQAML
+KSLDSLK
+>gnl|Smart|BAH Bromo adjacent homology domain
+REMHVNSTVIYLSDSDEPSSIEYLNGDNLTQVESGSALSSGGNEGIVSLDLNNPTKSTKRKGKRVTRTAVQEQNKRSICF
+FIGEPLSCEEAQERWRWRYELKMEKATSEFSGFTEQRIQCVYKFFSFIMERQATNHDKRRLFYSTVMNDNPVDCLISKVT
+VLQVSPRVGLKPNSIKSDYYFDMEYCVEYSTFQTLR
+>gnl|Smart|BASIC Basic domain in HLH proteins of MYOD family
+MELLSPPLRDIDLTGPDGSLCSFETADDFYDDPCFDSPDLRFFEDLDPRLVHVGALLKPEEHAHFSTAVHPGPGAREDEH
+VRAPSGHHQAGRCLLWACKACKRKTTNADRRKAA
+>gnl|Smart|BBC B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domains
+IRASILDMAHCIRTFTEEISDYSRKLVGIVQHIEGGEQIVEDGIGMAHTEHVPGTAENARSCIRAYFYDLHETLCRQEEM
+ALSVVDAHVREKLIWLRQQQEDMTILLSEVSAACLHCEKTLQQDDCRVVLAKQEITRLLETLQKQ
+>gnl|Smart|BBOX B-Box-type zinc finger
+RPLEKCSEHDERLKLYCKDDGTLSCVICRDSLKHASHNFLPI
+>gnl|Smart|BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions; (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
+LREAGDEFELRYRRAFSDLTSQLHITPGTAYQSFEQVVNELFRDGVNWGRIVAFFSFGGALCVESVDKEMQVLVSRIASW
+MATYLNDHLEPWIQENGGW
+>gnl|Smart|BH4 BH4 Bcl-2 homology region 4
+MSQSNRELVVDFLSYKLSQKGYSWSQF
+>gnl|Smart|BHL bacterial (prokaryotic) histone like domain
+MTKSELIERLATQQSHIPAKTVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHF
+KPGKELRDRAN
+>gnl|Smart|BIR Baculoviral inhibition of apoptosis protein repeat; Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes
+QTHAARMRTFMYWPSSVPVQPEQLASAGFYYVGRNDDVKCFCCDGGLRCWESGDDPWVEHAKWFPRCEFLIR
+>gnl|Smart|BowB Bowman-Birk type proteinase inhibitor
+CCDQCSCTKSMPPKCRCSDIRLNSCHSACKSCACTYSIPAKCFCTDINDFCYEPC
+>gnl|Smart|BPI1 BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain
+RISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSSQISMVPNVGLKFSISNANIKI
+SGKWKAQKRFLKMSGNFDLSIEGMSISADLKLGSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWLIQLFHKKIESALR
+NKMNSQVCEKVTNSVSSKLQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENH
+>gnl|Smart|BPI2 BPI/LBP/CETP C-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain
+AAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESKFRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLS
+VQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNY
+IVPILVLPRVNEKLQKGFPLPTPARVQLYNVVLQPHQNFLLFGA
+>gnl|Smart|BRCT breast cancer carboxy-terminal domain
+PDFFQGKHFFLYGEFPGDERRKLIRYVTAFNGELEDYMSDRVQFVITAQEWDPSFEEALMDNPSLAFVRPRWIYSCNEKQ
+>gnl|Smart|BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structure
+PKRKEFLDDLFSFMQKRGTPINRLPIMAKSVLDLYELYNLVIARGGLVDVINKKLWQEIIKGLHLPSS
+>gnl|Smart|BRLZ basic region leucin zipper
+GRDEALRLKQRRRTLKNRGYAQACRSKRLQQRRGLEAERARLAAQLDALRAEVARLARERDLYKARCDR
+>gnl|Smart|BROMO bromo domain
+EPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRSPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCK
+EYNAPESEYYKCANILEKFFFSKIKEAGL
+>gnl|Smart|BTB Broad-Complex, Tramtrack and Bric a brac; Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures
+ADVILVLQERVRIFAHKIYLSTSSSKFYDLFLMDLSEGELGGPSEPGGTHPEDHQGHSDQHHHHHHHHHGRDFLLRAASF
+DVCESVDEAGGSGPAGLRASTSDGILRGNGTGYLPGRGRVLSSWSRAFVSIQEEMAEDPLTYKSRLMVVVKMDSSIQPGP
+FRAVLKYLYTGELDENERDLMHIAHIAELLEVFDLRMMVANILNNEA
+>gnl|Smart|btg1 tob/btg1 family; The tob/btg1 is a family of proteins that inhibit cell proliferation
+MKEEIAATVVFLTMLVKKHKQLSKQKIEKFAAKLTTILFAKYKNHWYAENPMKGQAFRCIRINTYQAIDAVFEKACAESN
+VDFNDLGLPKEMTIWVDPFEVCCRYGEK
+>gnl|Smart|BTK Bruton's tyrosine kinase Cys-rich motif; Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region
+NSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILEN
+>gnl|Smart|C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains
+TTHNFARKTFLKLAFCDICQKFLLNGFRCQTCGYKFHEHCSTKVPTMC
+>gnl|Smart|C1Q Complement component C1q domain.; Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor
+VRSGSAKVAFSAIRSTNHEPSEMSNRTMIIYFDQVLVNIGNNFDSERSTFIAPRKGIYSFNFHVVKVYNRQTIQVSLMLN
+GWPVISAFAGDQDVTREAASNGVLIQMEKGDRAYLKLERGNLMGGWKYSTFSGFLVFPL
+>gnl|Smart|C2 Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles
+LLTVTIIKASNLKAMDLTGFSDPYVKASLISEGRRLKKRKTSIKKNTLNPTYNEALVFDVAPESVENVGLSIAVVDYDCI
+GHNEVIGVCRVGPEAADPHGREHWAEMLANPRKPVE
+>gnl|Smart|C4 C-terminal tandem repeated domain in type 4 procollagens; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome
+ANVIAVHSQTIQIPNCPNGWNSLWIGYSFAMHTGAGAEGGGQSLSSPGSCLEDFRATPFIECNGARGTCHYFANKFSFWL
+TTIEDDQQFRIPESETLKAGSLRTRVSRCQVCIRS
+>gnl|Smart|CA Cadherin repeats.; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium
+RIRSDRDKNLSLRYSVTGPGADQPPTGIFIINPISGQLSVTKPLDRELIARFHLRAHAVDINGNQVENPIDIVINVIDMN
+DNRP
+>gnl|Smart|CAD Domains present in proteins implicated in post-mortem DNA fragmentation
+RPFRVCDHKRTIRKGLTAATRQELLAKALETLLLNGVLTLVLEEDGTAVDSEDFFQLLEDDTCLMVLQSGQSW
+>gnl|Smart|CALCITONIN calcitonin; This family is formed by calcitonin, the calcitonin gene-related peptide, and amylin. They are short polypeptide hormones
+KRACNTATCVTHRLADFLSRSGGVGKNNFVPTNVGSKAFGRRR
+>gnl|Smart|Calx_beta Domains in Na-Ca exchangers and integrin-beta4; Domain in Na-Ca exchangers and integrin subunit beta4 (and some cyanobacterial proteins)
+VNITIIKEQASGIVSFEQPEYSVSRGDQVARIPVIRHILDNGKSQVSYSTQDNTAHGHRDYVPVEGELLFYPGETWKELQ
+VKLLELQEVDSLLRGRQVRRFQVQLS
+>gnl|Smart|CARD Caspase recruitment domain; Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain
+MDEADRRLLRRCRLRLVEELQVDQLWDVLLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDT
+GQDMLASFLRT
+>gnl|Smart|CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues
+SYKMDYPEMGLCIIINNKNFHKSTGMTSRSGTDVDAANLRETFRNLKYEVRNKNDLTREEIVELMRDVSKEDHSKRSSFV
+CVLLSHGEEGIIFGTNGPVDLKKITNFFRGDRCRSLTGKPKLFIIQACRGTELDCGIETDSGVDDDMACHKIPVDADFLY
+AYSTAPGYYSWRNSKDGSWFIQSLCAMLKQYADKLEFMHILTRVNRKVATEFESFSFDATFHAKKQIPCIVSMLTKELYF
+YH
+>gnl|Smart|CBF CCAAT-Binding transcription Factor
+TEDSTIYVNSKQYHGIIRRRQSRAKAAAVLDQKKLSSRCRKPYMHHSRHLHALRRPRGSGGRFLNT
+>gnl|Smart|CBS Domain in cystathionine beta-synthase and other proteins.; Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease
+DLVVAPAGITLKEANEILQRSKKGKLPIVNEDDELVAIIARTDLKKNRD
+>gnl|Smart|CCP Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII
+CEEPPTFEAMELIGKPKPYYEIGERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDAC
+>gnl|Smart|CH Calponin homology domain; Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p
+EKYAFVNWINKALENDPDCRHVIPMNPNTDDLFKAVGDGIVLCKMINLSVPDTIDERAINKKKLTPFIIQENLNLALNSA
+SAIGCHVVNIGAEDLRAGKPHLVLGLLWQIIKI
+>gnl|Smart|CheW Two component signalling adaptor domain
+VTIRLPLTLAIICALLVKVNNLVYAIPIANIDTILSISKEDIQRVQDRDVIVIRGEVIPVYRLWEVLQIEHKEELEEMEA
+VIVRVGNRKYGIVVDDLLGQDDIVIKSLGKVFSEVKEFSGAAILGDGSIALIINVSGIV
+>gnl|Smart|CHROMO Chromatin organization modifier domain
+GLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEER
+>gnl|Smart|ChSh Chromo Shadow Domain
+RGFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTWH
+>gnl|Smart|ChtBD1 Chitin binding domain
+PCGKDAGGRVCTNNYCCSKWGSCGIGPGYCGAGCQSGGC
+>gnl|Smart|ChtBD2 Chitin-binding domain type 2
+EICAPFHNGTINGRDRFPLRNCRYFAFCDTERPYLTLTQCPFNDLFNEATKTCEMHVNCGN
+>gnl|Smart|ChtBD3 Chitin-binding domain type 3
+SKDWAGGQPTHNEAGQSIVYKGNLYTANWYTASVPGSDSSWTQV
diff --git a/network/wwwblast/db/CDD/test_CDD_db.aux b/network/wwwblast/db/CDD/test_CDD_db.aux
new file mode 100644
index 00000000..ad8d7808
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.aux
@@ -0,0 +1,138 @@
+BLOSUM62
+11
+1
+1.275969e-01
+3.488586e-01
+407
+180825488
+1.000000
+249
+4.468556e-02
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+255
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+4.723063e-02
+36
+5.631683e-02
+48
+4.629887e-02
+139
+5.316101e-02
+116
+4.013166e-02
+115
+5.365433e-02
+84
+3.882144e-02
+73
+5.699629e-02
+43
+4.711526e-02
+106
+5.409688e-02
+91
+5.469011e-02
+242
+5.736400e-02
+66
+5.240911e-02
+49
+5.638631e-02
+60
+3.372790e-02
+113
+5.013248e-02
+139
+5.568152e-02
+52
+4.973259e-02
+61
+5.512530e-02
+39
+5.336284e-02
+61
+4.635138e-02
+44
+5.071739e-02
diff --git a/network/wwwblast/db/CDD/test_CDD_db.loo b/network/wwwblast/db/CDD/test_CDD_db.loo
new file mode 100644
index 00000000..9a98269d
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.loo
diff --git a/network/wwwblast/db/CDD/test_CDD_db.mn b/network/wwwblast/db/CDD/test_CDD_db.mn
new file mode 100644
index 00000000..59904059
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.mn
@@ -0,0 +1,65 @@
+14_3_3.mtx
+35EXOc.mtx
+4.1m.mtx
+53EXOc.mtx
+A1pp.mtx
+A4_EXTRA.mtx
+AAA.mtx
+AAI.mtx
+acidPPc.mtx
+ACTIN.mtx
+ADF.mtx
+ALBUMIN.mtx
+alkPPc.mtx
+ANATO.mtx
+ANK.mtx
+ANX.mtx
+AP2.mtx
+AP2Ec.mtx
+APPLE.mtx
+ARF.mtx
+ArfGap.mtx
+ARM.mtx
+AT_hook.mtx
+AXH.mtx
+B41.mtx
+B_lectin.mtx
+BAG.mtx
+BAH.mtx
+BASIC.mtx
+BBC.mtx
+BBOX.mtx
+BCL.mtx
+BH4.mtx
+BHL.mtx
+BIR.mtx
+BowB.mtx
+BPI1.mtx
+BPI2.mtx
+BRCT.mtx
+BRIGHT.mtx
+BRLZ.mtx
+BROMO.mtx
+BTB.mtx
+btg1.mtx
+BTK.mtx
+C1.mtx
+C1Q.mtx
+C2.mtx
+C4.mtx
+CA.mtx
+CAD.mtx
+CALCITONIN.mtx
+Calx_beta.mtx
+CARD.mtx
+CASc.mtx
+CBF.mtx
+CBS.mtx
+CCP.mtx
+CH.mtx
+CheW.mtx
+CHROMO.mtx
+ChSh.mtx
+ChtBD1.mtx
+ChtBD2.mtx
+ChtBD3.mtx
diff --git a/network/wwwblast/db/CDD/test_CDD_db.phr b/network/wwwblast/db/CDD/test_CDD_db.phr
new file mode 100644
index 00000000..e7ce2ef5
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.phr
@@ -0,0 +1 @@
+gnl|BL_ORD_ID|0 gnl|Smart|14_3_3 14-3-3 homologues; 14-3-3 homologues mediates signal transduction by binding to phosphoserine-containing proteins. They are involved in growth factor signalling and also interact with MEK kinasesgnl|BL_ORD_ID|1 gnl|Smart|35EXOc 3'-5' exonuclease; 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymesgnl|BL_ORD_ID|2 gnl|Smart|4.1m putative band 4.1 homologues' binding motifgnl|BL_ORD_ID|3 gnl|Smart|53EXOc 5'-3' exonucleasegnl|BL_ORD_ID|4 gnl|Smart|A1pp Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson & Fuji)gnl|BL_ORD_ID|5 gnl|Smart|A4_EXTRA amyloid A4; amyloid A4 precursor of Alzheimers diseasegnl|BL_ORD_ID|6 gnl|Smart|AAA ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignmentgnl|BL_ORD_ID|7 gnl|Smart|AAI Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain familygnl|BL_ORD_ID|8 gnl|Smart|acidPPc Acid phosphatase homologuesgnl|BL_ORD_ID|9 gnl|Smart|ACTIN Actin; ACTIN subfamily of ACTIN/mreB/sugarkinase/Hsp70 superfamilygnl|BL_ORD_ID|10 gnl|Smart|ADF Actin depolymerisation factor/cofilin -like domains; Severs actin filaments and binds to actin monomersgnl|BL_ORD_ID|11 gnl|Smart|ALBUMIN serum albumingnl|BL_ORD_ID|12 gnl|Smart|alkPPc Alkaline phosphatase homologuesgnl|BL_ORD_ID|13 gnl|Smart|ANATO Anaphylatoxin homologous domain; C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulinsgnl|BL_ORD_ID|14 gnl|Smart|ANK ankyrin repeats; Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structuregnl|BL_ORD_ID|15 gnl|Smart|ANX Annexin repeatsgnl|BL_ORD_ID|16 gnl|Smart|AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPsgnl|BL_ORD_ID|17 gnl|Smart|AP2Ec AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sitesgnl|BL_ORD_ID|18 gnl|Smart|APPLE APPLE domain; Four-fold repeat in plasma kallikrein and coagulation factor XI. Factor XI apple 3 mediates binding to platelets. Factor XI apple 1 binds high-molecular-mass kininogen. Apple 4 in factor XI mediates dimer formation and binds to factor XIIa. Mutations in apple 4 cause factor XI deficiency, an inherited bleeding disordergnl|BL_ORD_ID|19 gnl|Smart|ARF ARF-like small GTPases; ARF, ADP-ribosylation factor; Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop)gnl|BL_ORD_ID|20 gnl|Smart|ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF; Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFsgnl|BL_ORD_ID|21 gnl|Smart|ARM Armadillo/beta-catenin-like repeats; Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadheringnl|BL_ORD_ID|22 gnl|Smart|AT_hook DNA binding domain with preference for A/T rich regions; Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y)gnl|BL_ORD_ID|23 gnl|Smart|AXH domain in Ataxins and HMG containing proteins; unknown functiongnl|BL_ORD_ID|24 gnl|Smart|B41 Band 4.1 homologues; Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKsgnl|BL_ORD_ID|25 gnl|Smart|B_lectin Bulb-type mannose-specific lectingnl|BL_ORD_ID|26 gnl|Smart|BAG BAG domains, present in regulator of Hsp70 proteins; BAG domains, present in Bcl-2-associated athanogene 1 and silencer of death domainsgnl|BL_ORD_ID|27 gnl|Smart|BAH Bromo adjacent homology domaingnl|BL_ORD_ID|28 gnl|Smart|BASIC Basic domain in HLH proteins of MYOD familygnl|BL_ORD_ID|29 gnl|Smart|BBC B-Box C-terminal domain; Coiled coil region C-terminal to (some) B-Box domainsgnl|BL_ORD_ID|30 gnl|Smart|BBOX B-Box-type zinc fingergnl|BL_ORD_ID|31 gnl|Smart|BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions; (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulationgnl|BL_ORD_ID|32 gnl|Smart|BH4 BH4 Bcl-2 homology region 4gnl|BL_ORD_ID|33 gnl|Smart|BHL bacterial (prokaryotic) histone like domaingnl|BL_ORD_ID|34 gnl|Smart|BIR Baculoviral inhibition of apoptosis protein repeat; Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymesgnl|BL_ORD_ID|35 gnl|Smart|BowB Bowman-Birk type proteinase inhibitorgnl|BL_ORD_ID|36 gnl|Smart|BPI1 BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domaingnl|BL_ORD_ID|37 gnl|Smart|BPI2 BPI/LBP/CETP C-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domaingnl|BL_ORD_ID|38 gnl|Smart|BRCT breast cancer carboxy-terminal domaingnl|BL_ORD_ID|39 gnl|Smart|BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain; DNA-binding domain containing a helix-turn-helix structuregnl|BL_ORD_ID|40 gnl|Smart|BRLZ basic region leucin zippergnl|BL_ORD_ID|41 gnl|Smart|BROMO bromo domaingnl|BL_ORD_ID|42 gnl|Smart|BTB Broad-Complex, Tramtrack and Bric a brac; Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structuresgnl|BL_ORD_ID|43 gnl|Smart|btg1 tob/btg1 family; The tob/btg1 is a family of proteins that inhibit cell proliferationgnl|BL_ORD_ID|44 gnl|Smart|BTK Bruton's tyrosine kinase Cys-rich motif; Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) regiongnl|BL_ORD_ID|45 gnl|Smart|C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains); Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domainsgnl|BL_ORD_ID|46 gnl|Smart|C1Q Complement component C1q domain.; Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factorgnl|BL_ORD_ID|47 gnl|Smart|C2 Protein kinase C conserved region 2 (CalB); Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotamins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profilesgnl|BL_ORD_ID|48 gnl|Smart|C4 C-terminal tandem repeated domain in type 4 procollagens; Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndromegnl|BL_ORD_ID|49 gnl|Smart|CA Cadherin repeats.; Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calciumgnl|BL_ORD_ID|50 gnl|Smart|CAD Domains present in proteins implicated in post-mortem DNA fragmentationgnl|BL_ORD_ID|51 gnl|Smart|CALCITONIN calcitonin; This family is formed by calcitonin, the calcitonin gene-related peptide, and amylin. They are short polypeptide hormonesgnl|BL_ORD_ID|52 gnl|Smart|Calx_beta Domains in Na-Ca exchangers and integrin-beta4; Domain in Na-Ca exchangers and integrin subunit beta4 (and some cyanobacterial proteins)gnl|BL_ORD_ID|53 gnl|Smart|CARD Caspase recruitment domain; Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domaingnl|BL_ORD_ID|54 gnl|Smart|CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologuesgnl|BL_ORD_ID|55 gnl|Smart|CBF CCAAT-Binding transcription Factorgnl|BL_ORD_ID|56 gnl|Smart|CBS Domain in cystathionine beta-synthase and other proteins.; Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure [3]. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen diseasegnl|BL_ORD_ID|57 gnl|Smart|CCP Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR); The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIIIgnl|BL_ORD_ID|58 gnl|Smart|CH Calponin homology domain; Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24pgnl|BL_ORD_ID|59 gnl|Smart|CheW Two component signalling adaptor domaingnl|BL_ORD_ID|60 gnl|Smart|CHROMO Chromatin organization modifier domaingnl|BL_ORD_ID|61 gnl|Smart|ChSh Chromo Shadow Domaingnl|BL_ORD_ID|62 gnl|Smart|ChtBD1 Chitin binding domaingnl|BL_ORD_ID|63 gnl|Smart|ChtBD2 Chitin-binding domain type 2gnl|BL_ORD_ID|64 gnl|Smart|ChtBD3 Chitin-binding domain type 3
\ No newline at end of file
diff --git a/network/wwwblast/db/CDD/test_CDD_db.pin b/network/wwwblast/db/CDD/test_CDD_db.pin
new file mode 100644
index 00000000..515aefa7
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.pin
diff --git a/network/wwwblast/db/CDD/test_CDD_db.pn b/network/wwwblast/db/CDD/test_CDD_db.pn
new file mode 100644
index 00000000..1479a3e0
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.pn
@@ -0,0 +1,65 @@
+14_3_3.chk
+35EXOc.chk
+4.1m.chk
+53EXOc.chk
+A1pp.chk
+A4_EXTRA.chk
+AAA.chk
+AAI.chk
+acidPPc.chk
+ACTIN.chk
+ADF.chk
+ALBUMIN.chk
+alkPPc.chk
+ANATO.chk
+ANK.chk
+ANX.chk
+AP2.chk
+AP2Ec.chk
+APPLE.chk
+ARF.chk
+ArfGap.chk
+ARM.chk
+AT_hook.chk
+AXH.chk
+B41.chk
+B_lectin.chk
+BAG.chk
+BAH.chk
+BASIC.chk
+BBC.chk
+BBOX.chk
+BCL.chk
+BH4.chk
+BHL.chk
+BIR.chk
+BowB.chk
+BPI1.chk
+BPI2.chk
+BRCT.chk
+BRIGHT.chk
+BRLZ.chk
+BROMO.chk
+BTB.chk
+btg1.chk
+BTK.chk
+C1.chk
+C1Q.chk
+C2.chk
+C4.chk
+CA.chk
+CAD.chk
+CALCITONIN.chk
+Calx_beta.chk
+CARD.chk
+CASc.chk
+CBF.chk
+CBS.chk
+CCP.chk
+CH.chk
+CheW.chk
+CHROMO.chk
+ChSh.chk
+ChtBD1.chk
+ChtBD2.chk
+ChtBD3.chk
diff --git a/network/wwwblast/db/CDD/test_CDD_db.psq b/network/wwwblast/db/CDD/test_CDD_db.psq
new file mode 100644
index 00000000..d32afff0
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.psq
diff --git a/network/wwwblast/db/CDD/test_CDD_db.rps b/network/wwwblast/db/CDD/test_CDD_db.rps
new file mode 100644
index 00000000..e4382bc6
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.rps
diff --git a/network/wwwblast/db/CDD/test_CDD_db.sn b/network/wwwblast/db/CDD/test_CDD_db.sn
new file mode 100644
index 00000000..9f07e5fb
--- /dev/null
+++ b/network/wwwblast/db/CDD/test_CDD_db.sn
@@ -0,0 +1,65 @@
+14_3_3.csq
+35EXOc.csq
+4.1m.csq
+53EXOc.csq
+A1pp.csq
+A4_EXTRA.csq
+AAA.csq
+AAI.csq
+acidPPc.csq
+ACTIN.csq
+ADF.csq
+ALBUMIN.csq
+alkPPc.csq
+ANATO.csq
+ANK.csq
+ANX.csq
+AP2.csq
+AP2Ec.csq
+APPLE.csq
+ARF.csq
+ArfGap.csq
+ARM.csq
+AT_hook.csq
+AXH.csq
+B41.csq
+B_lectin.csq
+BAG.csq
+BAH.csq
+BASIC.csq
+BBC.csq
+BBOX.csq
+BCL.csq
+BH4.csq
+BHL.csq
+BIR.csq
+BowB.csq
+BPI1.csq
+BPI2.csq
+BRCT.csq
+BRIGHT.csq
+BRLZ.csq
+BROMO.csq
+BTB.csq
+btg1.csq
+BTK.csq
+C1.csq
+C1Q.csq
+C2.csq
+C4.csq
+CA.csq
+CAD.csq
+CALCITONIN.csq
+Calx_beta.csq
+CARD.csq
+CASc.csq
+CBF.csq
+CBS.csq
+CCP.csq
+CH.csq
+CheW.csq
+CHROMO.csq
+ChSh.csq
+ChtBD1.csq
+ChtBD2.csq
+ChtBD3.csq
diff --git a/network/wwwblast/db/test_aa_db b/network/wwwblast/db/test_aa_db
new file mode 100644
index 00000000..e88ac6cf
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db
@@ -0,0 +1,1000 @@
+>gi|6693791|gb|AAF24984.1|AF082179_1 (AF082179) HepA-related protein HARP [Homo sapiens]
+MSLPLTEEQRKKIEENRQKALARRAEKLLAEQHQRTSSGTSIAGNPFQAKQGPSQNFPRESCKPVSHGVI
+FKQQNLSSSSNADQRPHDSHSFQAKGIWKKPEEMPTACPGHSPRSQMTLTGISPPLAQSPPEVPKQQLLS
+YELGQGHAQASPEIRFTPFANPTHKPLAKPKSSQETPAHSSGQPPRDAKLEAKTAKASPSGQNISYIHSS
+SESVTPRTEGRLQQKSGSSVQKGVNSQKGKCVRNGDRFQVLIGYNAELIAVFKTLPSKNYDPDTKTWNFS
+MNDYSALMKAAQSLPTVNLQPLEWAYGSSESPSTSSEGQAGLPSAPSLSFVKGRGMLISRAYFEADISYS
+QDLIALFKQMDSRRYDVKTRKWSFLLEEHSKLIAKVRCLPQVQLDPLPTTLTLAFASQLKKTSLSLTPDV
+PEADLSEVDPKLVSNLMPFQRAGVNFAIAKGGRLLLADDMGLGKTIQAICIAAFYRKEWPLLVVVPSSVR
+FTWEQAFLRWLPSLSPDCINVVVTGKDRLTAGLINIVSFDLLSKLEKQLKTPFKVVIIDESHFLKNSRTA
+RCRAAMPVLKVAKRVILLSGTPAMSRPAELYTQIIAVKPTFFPQFHAFGLRYCDAKRMPWGWDYSGSSNL
+GELKLLLEEAVMLRRLKSDVLSQLPAKQRKIVVIAPGRINARTRAALDAAAKEMTTKDKTKQQQKDALIL
+FFNRTAEAKIPSVIEYILDLLESGREKFLVFAHHKVVLDAITQELERKHVQHIRIDGSTSSAEREDLCQQ
+FQLSERHAVAVLSITAANMGLTFSSADLVVFAELFWNPGVLIQAEDRVHRIGQTSSVGIHYLVAKGTADD
+YLWPLIQEKIKVLAEAGLSETNFSEMTESTDYLYKDPKQQKMYDLFQKSFEKEGSDMELVEAAESFDPGS
+GSGTSGSSSQNMGDTLDESSLTASPQKKRRFEFFDNWDSFTSPL
+>gi|6693793|gb|AAF24985.1|AF088884_1 (AF088884) HepA-related protein Harp [Mus musculus]
+MSLPLTEEQRKKIEENRQKALARRAEKLSEQPQSAASGSSAAGPSQSKQGSLLNLLAEPSKPVGHASIFK
+QQNLSNSFPTDQRPHSSRCSQPSPAEETTGLWKTQGEMSTACPKPNPSPPGASNQPLLGYKSSEGQPQAT
+WDTGASSSGPFPRDPELEAKAARPSTSRQSISDSFYVLGGKTPRTEGRPPNILQTTPQNTGFLRGACIKT
+GDRFRVKIGYNQELIAVFKSLPSRHYDSFTKTWDFSMSDYRALMKAVERLSTVSLKPLDEAGGSVGGQTS
+LPSAPSLTFVTGKCMLISRVRFEVDIGYSEAVIGLFKQMESRSYDIKTRKWSFLLEEHNKLIARSRELKQ
+VQLDPLPKTVTLAFASQLEKTSPKLKADVPEADLSGVDAKLVSSLMPFQREGVSFAISKRGRLLLADDMG
+LGKTVQAICIAAFYRKEWPLLVVVPSSVRFTWEQAFLRWLPSLSPENINVVVTGKGRLTAGLVNIVSFDL
+LCKLERQLKTPFKVVIIDESHFLKNIKTARCRAAVPILKVAKRVILLSGTPAMSRPAELYTQIIAVKPTF
+FPQFHAFGLRYCDAKRLPWGWDYSGSSNLGELKLLLEEAIMLRRLKSDVLSQLPAKQRKMVVVNPGRISS
+RAKAALDAAAKEMTKDKTKQQQKEALLVFFNRTAEAKIPCVVEYILDLLDSGREKFLVFAHHKVILDAVA
+KELERKNVQHIRIDGSRPTRARELKCQRFQLSKGHTVALLSIPAANMGLTFSTADLVVFAELFWNPGVLI
+QAEDRVHRIGQTNSVSIHYLVAKGTADDYLWPLIQEKIKVLGEAGLSETNFSEMTEATDYVHKAPKQKTI
+YDLFQQSFEDDGNDMEFLEAAESFEIKNTSGTSGNISQDLGDLLDEDEGSPPKKSRFEFFDNWDSFSSPF
+>gi|6693798|gb|AAF24986.1|AF116242_1 (AF116242) K-Cl cotransporter KCC3 [Homo sapiens]
+MHPPETTTKMASVRFMVTPTKIDDIPGLSDTSPDLSSRSSSRVRFSSRESVPETSRSEPMSEMSGATTSL
+ATVALDPPSDRTSHPQDVIEDLSQNSITGEHSQLLDDGHKKARNAYLNNSNYEEGDEYFDKNLALFEEEM
+DTRPKVSSLLNRMANYTNLTQGAKEHEEAENITEGKKKPTKTPQMGTFMGVYLPCLQNIFGVILFLRLTW
+VVGTAGVLQAFAIVLICCCCTMLTAISMSAIATNGVVPAGGSYFMISRALGPEFGGAVGLCFYLGTTFAA
+AMYILGAIEIFLVYIVPRAAIFHSDDALKESAAMLNNMRVYGTAFLVLMVLVVFIGVRYVNKFASLFLAC
+VIVSILAIYAGAIKSSFAPPHFPVCMLGNRTLSSRHIDVCSKTKEINNMTVPSKLWGFFCNSSQFFNATC
+DEYFVHNNVTSIQGIPGLASGIITENLWSNYLPKGEIIEKPSAKSSDVLGSLNHEYVLVDITTSFTLLVG
+IFFPSVTGIMAGSNRSGDLKDAQKSIPIGTILAILTTSFVYLSNVVLFGACIEGVVLRDKFGDAVKGNLV
+VGTLSWPSPWVIVIGSFFSTCGAGLQSLTGAPRLLQAIAKDNIIPFLRVFGHSKANGEPTWALLLTAAIA
+ELGILIASLDLVAPILSMFFLMCYLFVNLACALQTLLRTPNWRPRFRYYHWALSFMGMSICLALMFISSW
+YYAIVAMVIAGMIYKYIEYQGAEKEWGDGIRGLSLSAARFALLRLEEGPPHTKNWRPQLLVLLKLDEDLH
+VKHPRLLTFASQLKAGKGLTIVGSVIVGNFLHNYGEALAAEQTIKHLMEAEKVKGFCQLVVAAKLREGIS
+HLIQSCGLGGMKHNTVVMGWPNGWRQSEDARAWKTFIGTVRVTTAAHLALLVAKNISFFPSNVEQFSEGN
+IDVWWIVHDGGMLMLLPFLLKQHKVWRKCSIRIFTVAQLEDNSIQMKKDLATFLYHLRIEAEVEVVEMHD
+SDISAYTYERTLMMEQRSQMLRHMRLSKTERDREAQLVKDRNSMLRLTSIGSDEDEETETYQEKVHMTWT
+KDKYMASRGQKAKSMEGFQDLLNMRPDQSNVRRMHTAVKLNEVIVNKSHEAKLVLLNMPGPPRNPEGDEN
+YMEFLEVLTEGLERVLLVRGGGSEVITIYS
+>gi|6693800|gb|AAF24987.1|AF121349_1 (AF121349) HOAR-like protein [Neodiprion sertifer nucleopolyhedrovirus]
+EFSFTKTVEYARIPVNEYQPDGPLCDDCTVSQEPDDDKITDMLNQIKDQIQETTNDTMKQIELITGDGLS
+TLQNDLQTLGTNISTNLQSQSDASALYIETLKDDAVAAIENAKTSVDEYLISSIQTAIDAINVAATQSVT
+AVEDKAKTAIESISENIISQLEVNNDAITSELNKLSSEVSDNIDTITSDVTTAFDNIQTALQKSETSTVS
+GINDTGIVIEKLIKFNEDSITSAINTTVTNLTDLLSTAENTVIDTINNVIS
+>gi|6693801|gb|AAF24988.1|AF121349_2 (AF121349) ORF22 [Neodiprion sertifer nucleopolyhedrovirus]
+MLFYFIVITILVLLGIYIFTKPLLDTIYVIQTAQTKYVDTIDENVEAIEKNLAESRYVPLENLANIDINN
+STELMNGENKCFAAPIRVSNVETSTFDCTTVCENESASYFFVDENDIFVINGSRLSSGGYCSTTALPTKC
+NRETSIVLYSVNTWTCIAEDPRFFAGESNSVQIAGRQHSRFILSGYEQYNILYDKLLENEVDITRNTLRT
+SWDELLDDGTRRFVVLCNALDVNYNEMFVNPYNEIECLPNVCTNVQYAHRDVKPDFVNGVCDCGDYSVTR
+MQHVTSGDETSLCANIINESDYDNNVYKFRSDCLKMTDVVSKLETDGVRLFCPPDVFNTTGDAAYQVEVK
+GFACRTNNGVDELTYRLENDFGDRLTYINDRIIS
+>gi|6693802|gb|AAF24989.1|AF121349_3 (AF121349) late expression factor 2 [Neodiprion sertifer nucleopolyhedrovirus]
+MENEIIYIKSADELKRAQNDDLRNVYVHYTLYSGILSPLQTLDKTRLYVFVKNVNDPNLKPKNVNDIKSP
+SKNHSYKRQRYPCFNTISGSTIHKICNVMKPPPCVRHALKLIDERPMKHRFQQRFVVQTYMSRKYLCESC
+TDNECLNQILSELYHNEKKCMTQLKHCTNNKIKPYNCSKMQTLGLCNVAVKCSCTNLLSW
+>gi|6693803|gb|AAF24990.1|AF121349_4 (AF121349) late expression factor 5 [Neodiprion sertifer nucleopolyhedrovirus]
+MPPCSEKTLKDIEEIFLKFRRKKKWEDLIRYLKYKQPKCVKTFNLTGTGHKYHAMWAYNPITDKREKKQI
+SLDVMKIQELHRITNNNSKLYVEIRKIMTDDHRCPCEEIKNYMQQIAEYKNNRSNKVFNTPPTKIVPNAL
+EKILKNFTINLMIDKKPKKKITKSAHTIKHPPVLNIDYEHTLEFAGQTTVKEICKHASLGDTIEIQNRSF
+DEMVNLYTTCVQCKQMYKIQ
+>gi|6693805|gb|AAF24991.1| (AF125506) astacin family metalloendopeptidase FARM-1 [Hydra vulgaris]
+MSSSNHIHVLRAIDEYHKHTCLKFVKRTNQDAYLSFYPGGGCSSLVGYVRGRINDVSLAGGCLRLGTVMH
+EIGHSIGLYHEQSRPDRDDHVTIIWNNIQSNMRFNFDKFDRNKINSLGFPYDYESMMHYESNAFGGGQVT
+IRTKDPSKQKLIGNRQGFSEIDKQQINAMYNCNRGGSTLPPSVPPTVSPVAQCVEGQDLDNRCLGWATSG
+YCTATDPAHLETMKKKCCKSCKESAICNDKNTRCDEWAKKGECKANPNWMLGNCSKSCLVC
+>gi|6693816|gb|AAF24994.1|AF129447_1 (AF129447) RpoB [Klebsiella ornithinolytica]
+AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI
+GLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFVEDLVTCRSK
+GESSLFSRDQVDYMDVSTQQVVSVGGSSERVL
+>gi|6693818|gb|AAF24995.1|AF129448_1 (AF129448) RpoB [Klebsiella terrigena]
+AAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI
+GLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDDEGHFEEDLVTCRSK
+GESSLFSRDQVDYMDVSTQQVVSVGASLIP
+>gi|6693824|gb|AAF24998.1|AF134213_1 (AF134213) ubiquitin-specific protease [Homo sapiens]
+MTVEQNVLQQSAAQKHQQTFLNQLREITGINDTQILQQALKDSNGNLELAVAFLTAKNAKTPQQEETTYY
+QTALPGNDRYISVGSQADTNVIDLTGDDKDDLQRAIALSLAESNRAFRETGITDEEQAISRVLEASIAEN
+KACLKRTPTEVWRDSRNPYDRKRQDKAPVGLKNVGNTCWFSAVIQSLFNLLEFRRLVLNYKPPSNAQDLP
+RNQKEHRNLPFMRELRYLFALLVGTKRKYVDPSRAVEILKDAFKSNDSQQQDVSEFTHKLLDWLEDAFQM
+KAEEETDEEKPKNPMVELFYGRFLAVGVLEGKKFENTEMFGQYPLQVNGFKDLHECLEAAMIEGEIESLH
+SENSGKSGQEHWFTELPPVLTFELSRFEFNQALGRPEKIHNKLEFPQVLYLDRYMHRNREITRIKREEIK
+RLKDYLTVLQQRLERYLSYGSGPKRFPLVDVLQYALEFASSKPVCTSPVDDIDASSPPSGSIPSQTLPST
+TEQQGALSSELPSTSPSSVAAISSRSVIHKPFTQSRIPPDLPMHPAPRHITEEELSVLESCLHRWRTEIE
+NDTRDLQESISRIHRTIELMYSDKSMIQVPYRLHAVLVHEGQANAGHYWAYIFDHRESRWMKYNDIAVTK
+SSWEELVRDSFGGYRNASAYCLMYINDKAQFLIQEEFNKETGQPLVGIETLPPDLRDFVEEDNQRFEKEL
+EEWDAQLAQKALQEKLLASQKLRESETSVTTAQAAGDPEYLEQPSRSDFSKHLKEETIQIITKASHEHED
+KSPETVLQSAIKLEYARLVKLAQEDTPPETDYRLHHVVVYFIQNQAPKKIIEKTLLEQFGDRNLSFDERC
+HNIMKVAQAKLEMIKPEEVNLEEYEEWHQDYRKFRETTMYLIIGLENFQRESYIDSLLFLICAYQNNKEL
+LSKGLYRGHDEELISHYRRECLLKLNEQAAELFESGEDREVNNGLIIMNEFIVPFLPLLLVDEMEEKDIL
+AVEDMRNRWCSYLGQEMEPHLQEKLTDFLPKLLDCSMEIKSFHEPPKLPSYSTHELCERFARIMLSLSRT
+PADGR
+>gi|6693827|gb|AAF24999.1| (AF141320) endo-inulinase [Pseudomonas mucidolens]
+MHNTEDTGLIAYWSFDEESGKTAVDVIGKMNDSIDYVFNHARFKASSDPQRRKGISGNALLFDGYSTWIK
+RSADQIGKPENALTLEAWVAPRSYEWGDEQRLSAIVNQHDREKKEGFILGMYRHGTWSLQLGLDHEWIEV
+WSEDHPLPKNEWSYVVATYDKKTSMLKLACPSMLKLYLNGVEVASKQTTAHSTITPSRQDLLIGKNNQAV
+VLAGVFSLNMFNGLIDEIKIYNRALSSDEIASSFHRYLVPYGGKIPSIPYDHLKLDRSLLADDRHRPQYH
+VSPPAHWMNEPHAPIYFNGQYHLFYQHNPQGPYWHQIHWGHWVSDDLVHWRDLPVALSPEKNAVDPDGDW
+SGSATYDEHGLPVLFFTAGDDSAKPNQRVGLARSTFAQDGDNDLVHWVKHPTPVVVQQQGVGKFGDFRDP
+FVWKDGDTWYMLVGSGTDGEGGTALAYTSKNLTEWEYRGPFYISDHKNYPYLGKVWELPVLLPLGKDKKG
+HDKHVFLISPVGAGADVEVFYWIGTFDKEQFRFIPDQNEPQLIDVGDSHFTGPSGMVDPNTGRKILFTIA
+QGERTPALDYSAGWAHNGGLPVSLSLREDGRLGVEPIEELKSLRGKKLVSFTKKSAEEANDLLTNVKGDM
+LEIILELEPGTAKQFGIKVRRSPGGEEETLLYYNTEASTLNVNRMKTTLDNFERSKGIQGGKLELNGENL
+KLHIYLDRSMIEAYANGLKSLTTRAYPSRPDSLGLQIWGDGSVSVKSMEVWEMNSAFGPTVSAYIPEQHA
+DGVQTK
+>gi|6693829|gb|AAF25000.1|AF153207_1 (AF153207) proline dehydrogenase [Pseudomonas putida]
+MATTTLGVKLDDPTRERLKAAAQSIDRTPHWLIKQAIFNYLEKLEGGATLTELNGHASNPADDAGEVQAD
+HSHQCFLEFAESILPQSVLRSAITAAYRRPEQEVVPMLLEQARLSAPLADATNKLAASIAEKLRNQKSVG
+GRAGIVQGLLQEFSLSSQERRGVCLAEALLRIPDKGTRDALIRDKISTGNWQPHLGNSPSLFVNAATWGL
+LLTGKLVSTHNETGLTSSLTRIIGKSGEPMIRKGVDMAMRLMGEQFVTGETIAEALANASRFEAKGFRYS
+YDMLGEAALTEHDAQKYLASYEQAIHSIGKASHGRGIYEGPGISIKLSALHPRYSRAQYERVMEELYPRL
+LSLTLLAKQYDIGLNIDAEEADRLELSLDLLERLCFEPSLAGWNGIGFVIQAYQKRCPYLINYFFDLAKR
+TPHRLIIRLLKGAYWDSEIKRAQVEGLEGYPVYTRKVYTDVSYVACARKLLAVPEAIYPQFATHNAHTLS
+AIYHIAGQNYYPGQYEFQCLHGMGEPLYEQVVGKIADGKLNRPCRVYAPVGTHETLLAYLVRRLLENGAN
+TSFVNRIADHSISIQELVADRWPASIAWVPRKGSIGLPHPRIPLPRDLYGTERAKLAGIEMANEHRLGLL
+SCAMVATAHKQWEAAPLLACAARESAAAPVLNPADHRNVVGHVQEATVAKFDNAIHCALNPAPIWQATPP
+AERAAILERTADLMEAEIHPLMGLLIREAGKTFPNAIAELREAVDFLRYYAVQALNDFSNDAHRPLGPVV
+CISPWNFPLAIFTGQVAAALAAGNPVLAKPAEQTPLIAAQAVRLLLEAGIPEGVLQLLPGRGETVGAGLV
+GDERVKGVMFTGSTEVARLLQRNVAGRLDNQGRPIPLIAETGGQNAMIVDSSALTEQVVIDVVSSAFDSA
+GQRCSALRVLCLQEDSADRVIEMLKGAMAESRLGCPDRLAVDIGPVIDAEAKAGIEKHIQGMREKGRPVY
+QVAIADAAEIKRGTFVMPTLIELDSFDELKREIFGPVLHVVRYNRRNLDQLIEQINNSGYGLTLGVHTRI
+DETIAKVVETATPATCRHRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLYRLLSTRPADAIGRHFQQQDG
+EGTPDRTLHEQLVKPLHGLKAWAENNQLADLAALCSQFASQSQSGIARLLPGPTGERNSYTILPREHVLC
+LADNETDLLAQFAAVLAVGSSAVWVDGEPGKALRARLPRELQAKVKLVADWNKDEVAFDAVIHHGDSDQL
+RGVCQQVAKRAGAIVGVHGLSSGDHQIALERLVIERAVSVNTAAAGGNASLMTIG
+>gi|6693830|gb|AAF25001.1|AF153207_2 (AF153207) proline permease [Pseudomonas putida]
+MGNPLTITFVIYIAAMVLIGFAAYRATNNLSDYILGGRSLGSVVTALSAGASDMSGWLLMGLPGAIYFAG
+LSEAWIAIGLTVGAYLNWLFVAGRLRVQTEHNGDALTLPDYFSSRFEDNSGLLRIISAIVILVFFTIYCA
+SGIVAGARLFESTFGMSYETALWAGAAATIAYTFVGGFLAVSWTDTVQASLMIFALILTPVIVLISTGGF
+DQTFAAIEAVNRRNFDMLKGATFIGIISLMGWGLGYFRPPHILARFMAADSVNSIAKARRISMTWMILCL
+AGTCAVGFCGIAYFSAHPELAGPVSENHKRVFIELAKILFNPWVAGVLLSAILAAVMITLSCQLLVCSSA
+LTENFYKAFLRKNASQVELVWVGRLMVLAVALIAIAMAANPENRVLGLVAYAWAGFGAAFGPVVLISVLW
+KGMTRNGALAGIVVGALTVILWKNFDTLGLYEIIPGFLFASIAIVLVSKLGSPSQTMVKRFEAADAAYHA
+DK
+>gi|6693832|gb|AAF25002.1|AF156878_1 (AF156878) opioid growth factor receptor [Rattus norvegicus]
+MDDPDCDSTWEEESEEDGEDGQADDTTDEDTGDDDGDAEEARPSLFQSRMTGYRNWRAMQDMQRYRHNYP
+DLTDQDCNGDMCNLSFYKNEICFQPNGALIEDILQNWKDNYDLLEENHSYIQWLFPLREPGVNWHAKPLT
+LKEVEAFKSSKEVRERLVRAYELMLGFYGFHLEDRGTGAVCRAQNFQPRFHNLNSHSHNNLRITRILKSL
+GELGLEHYQAPLVRFFLEETLVQHKLPSVRQSALDYFLFAVRCRHQRRELVYFAWEHFKPRREFVWGPRD
+KLRRFKPQTIPQPLTGPGQADKDEGSRDPSQEAGTQGRTCGSGRDLSGDSGTAEDPSLLNTKPSDGGTLD
+GNQRDEAKSLSPKESKKRKLEGNRQEQVPGEADPQGVSEVEKIALNLEECALSPISQEPREAEPPCPVAR
+VANEVRKRRKVEEGAEGDGVVSNTQMQASALPPTPSECPEAQKDGNGPEDSNSQVGAEDSKSQVGPEDPN
+SQVGLEDPNSQVGPEDPNSQVGPEDPNSQVGPEDPNSQVGPEDPNSQVVGPEQAASKSPVEDPDSDTMGT
+SVDESEELARIEASAEPPKP
+>gi|6693834|gb|AAF25003.1|AF156981_1 (AF156981) SNIP-a [Rattus norvegicus]
+MQPWQCLRRFALAWWERTAEGRARSPREEVGPRDPGGRGEPDPERSSPPMLSADDAEYPREYRTLGGGGS
+GGSGGRRFSNVGLVHTSERRHTVIAAQSLEALSGLQKADADRKRDAFMDHLKSKYPQHALALRGQQDRMR
+EQQPNYWSFKTRSSRHTQGAQPGLADQAAKLSYASAESLETMSEAELPLGFSRMNRFRQSLPLSRSASQT
+KLRSPGVLFLQFGEETRRVHITHEVSSLDTLHALIAHMFPQKLTMGMLKSPNTAILIKDEARNVFYELED
+VRDIQDRSIIKIYRKEPLYAAFPGSHLTNGDLRREMVYASRESSPTRRLNNLSPASHLASSSPPPGLPSG
+LPSGLPSGSPSRSRLSYAGGRPPSYAGSPVHHAAERLGGAPTSQGVSPSPSAILERRDVKPDEDLAGKAG
+GMVLVKGEGLYADPYGLLHEGRLSLAAAAGDPFAYPGAGGLYKRGSVRSLSTYSAAALQSDLEDSLYKAG
+AGGPLYGDGYGFRLPPSSPQKLADVSAPSGGPPPPHSPYSGPPSRGSPVRQSFRKDSGSSSVFAESPGGK
+ARSTGASTAGAPPSELFPGPGERSLVGFGPPVPAKDTETRERMEAMEKQIASLTGLVQSALLRGSEPETP
+SEKIEGSNGAATPSAPVCGSGSRSSGATPVSGPPPPAVSSTPAGQPTAVSRLQMQMHLRGLQNSASDLRG
+QLQQLRKLQLQNQESVRALLKRTEAELSMRVSEAARRQEDPLQRQRTLVEEERLRYLNDEELITQQLNDL
+EKSVEKIQRDVAHNHRLVPGPELEEKALVLKQLGETLTELKAHFPGLQSKMRVVLRVEVEAVKFLKEEPQ
+RLDGLLKRCRVVTDTLAQIRRQVDEGVWPPPNNLLNQSPKKVAAETDFSKGLDFEIPPPSPPLNLHELSG
+PAEGTPLTPKSGNPTKGLDAPSKRNMDKAVSVEAAERDWEEKRAALTQYSAKDINRLLEETQAELLKAIP
+DLDCASKTHPGPTPTPDHKPPKAPHGQKAAPRTEPSGRRGSDELTVPRYRTEKPSKSPPPPPPRRSFPSS
+HGLTTTRTGEVVVTSKKDSVFIKKAESEELEIQKPQVKLRRAVSEVVRPASTPPIMASAIKDEDDEERII
+AELESGGGSVPPMKVVTPGASRLKAAQGPAGSPDKGKHGKQRTEYMRIQAQQQ
+>gi|6693836|gb|AAF25004.1|AF156982_1 (AF156982) SNIP-b [Rattus norvegicus]
+MQPWQCLRRFALAWWERTAEGRARSPREEVGPRDPGGRGEPDPERSSPPMLSADDAEYPREYRTLGGGGS
+GGSGGRRFSNVGLVHTSERRHTVIAAQSLEALSGLQKADADRKRDAFMDHLKSKYPQHALALRGQQDRMR
+EQQPNYWSFKTRSSRHTQGAQPGLADQAAKLSYASAESLETMSEAELPLGFSRMNRFRQSLPLSRSASQT
+KLRSPGVLFLQFGEETRRVHITHEVSSLDTLHALIAHMFPQKLTMGMLKSPNTAILIKDEARNVFYELED
+VRDIQDRSIIKIYRKEPLYAAFPGSHLTNGDLRREMVYASRESSPTRRLNNLSPASHLASSSPPPGLPSG
+LPSGLPSGSPSRSRLSYAGGRPPSYAGSPVHHAAERLGGAPTSQGVSPSPSAILERRDVKPDEDLAGKAG
+GMVLVKGEGLYADPYGLLHEGRLSLAAAAGDPFAYPGAGGLYKRGSVRSLSTYSAAALQSDLEDSLYKAG
+AGGPLYGDGYGFRLPPSSPQKLADVSAPSGGPPPPHSPYSGPPSRGSPVRQSFRKDSGSSSVFAESPGGK
+ARSTGASTAGAPPSELFPGPGERSLVGFGPPVPAKDTETRERMEAMEKQIASLTGLVQSALLRGSEPETP
+SEKIEGSNGAATPSAPVCGSGSRSSGATPVSGPPPPAVSSTPAGQPTAVSRLQMQMHLRGLQNSASDLRG
+QLQQLRKLQLQNQESVRALLKRTEAELSMRVSEAARRQEDPLQRQRTLVEEERLRYLNDEELITQQLNDL
+EKSVEKIQRDVAHNHRLVPGPELEEKALVLKQLGETLTELKAHFPGLQSKMRVVLRVEVEAVKFLKEEPQ
+RLDGLLKRCRVVTDTLAQIRRQVDEGVWPPPNNLLNQSPKKVAAETDFSKGLDFEIPPPSPPLNLHELSG
+PAEGTPLTPKSGNPTKGLDAPSKRNMDKAVSVEAAERDWEEKRAALTQYSAKDINRLLEETQAELLKAIP
+DLDCASKTHPGPTPTPDHKPPKAPHGQKAAPRTEPSGRRGSDELTVPRYRTEKPSKSPPPPPPRRSFPSS
+HGLTTTRTGEVVVTSKKDSVFIKKAESEELEIQKPQVKLRRAVSEVVRPASTPPIMASAIKDEDDEERII
+AELESGGGSVPPMKVVTPGASRLKAAQGPAGSPDKGKHGKQRTEYMRIQAQQQVRVGYQAPRPLEGCTPR
+LCYMPLS
+>gi|6693838|gb|AAF25005.1|AF158184_1 (AF158184) 14-kDa diagnostic antigen [Taenia solium]
+MRAYIVLLALTVFVVTVSAEKNKPKDVANSTKKGIEYVHEFFHEDPIGKQIAQLAKEWKEAMLEDKGKIR
+TSLVEHCKGPKKKTA
+>gi|6693854|gb|AAF25008.1|AF176679_1 (AF176679) salmonase [Gloydius halys brevicaudus]
+MVLIRVLVNFLILQLSYAQKSSELVIGGDECNINEHRFLALLYSERFQCGGTLINEEWVLTAAHCDMRNM
+YIYLGVHNVSVQYDDEQRRYPKKKYFRLSSRNYNQWDKDIMLIRLNRPLRNSAHIAPLSLPSNPPSVGSV
+CRIMGWGTITSPQVTFPDVLHCANINIFDYEVCRAAYPELPATRRTLCAGILEGGKDSCNGDSGGPLICN
+GQFQGIAYWGADTCAQPREPGLYTKVFDYIDWIQSIIAGNTAVTCPP
+>gi|6693856|gb|AAF25009.1|AF177945_1 (AF177945) superoxide dismutase [Nostoc commune]
+MAFVQDPLPFDINALDPYGMKAETFEYHYGKHHKAYVDNLNKLTEGTELANKSLEEVIKTSFNDSSKAGI
+FNNAAQVWNHTFFWNSLKPAGGGAPTGDLAARIDKDFGSFDKFKEEFSNAAATQFGSGWSWLIDDGGTLK
+VIKTPNAENPLAHGKKALLTLDVWEHAYYIDFRNARPAFIKNFLDNLVNWDFAAENLAKA
+>gi|6693870|gb|AAF25010.1|AF179404_1 (AF179404) UDP-glucuronosyltransferase UGT2B15 [Homo sapiens]
+MSLKWTSVFLLIQLSCYFSSGSCGKVLVWPTEYSHWINMKTILEELVQRGHEVTVLTSSASTLVNASKSS
+AIKLEVYPTSLTKNDLEDSLLKILDRWIYGVSKNTFWSYFSQLQELCWEYYDYSNKLCKDAVLNK
+>gi|6693872|gb|AAF25011.1| (AF181288) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEDIVIRSSNFTNNVKTIIVQLNESVQINCTRPNNNTRRSISIGPGRAFYTTG
+EIIGEIRKAHCNISKAKWGKTLEQIARKLREQFKNRTIAFNQSSGGDPEI
+>gi|6693874|gb|AAF25012.1| (AF181289) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAKEEVVIRSENFTNNAKVIIVQLNESVQIHCIRPNNNTRRSITIGPGRAFYGTD
+IIGDIRQAHCNISEVGWNKTLKQIVKKLREQFGGNKTIIFNQSSGGDPEI
+>gi|6693876|gb|AAF25013.1| (AF181290) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIKSENFTDNDETIIVQLNESVVINCTRPNNNTRRSISIGPGRAFYATG
+DIIGNIRQAYCNISKEKWENTLKQVAKKLREKFNTTTIVFNRSSGGDPEI
+>gi|6693878|gb|AAF25014.1| (AF181291) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNETVVINCTRPNNNTRRSIPIGPGRAFYATG
+DIIGDIRQAHCNISREDWNNTLKYIVDKLREQFGVNKTIIFNQSSGGDPEI
+>gi|6693880|gb|AAF25015.1| (AF181292) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENLTNNAKTIIVHLNESVQINCTRPNNNTRRSIHIGPGRAFYGTD
+VIGDIRQAHCNISGTKWNDTLKKVVDKLREHFNKTIVFKPSSGGDPQI
+>gi|6693882|gb|AAF25016.1| (AF181293) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENITDNAKTIIVQLKKAVNITCMRPSNNTRRGIPIGPGRAFYTTG
+HVTGDIRQAHCNLSRAQWNNTLKQMVDKLREQFGNKTISFNQSSGGDPEI
+>gi|6693884|gb|AAF25017.1| (AF181294) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSDNFSDNAKIIIVQLNKTVEINCTRPNNNTRKSIPIGPGRAFYATG
+DIIGDIRQAHCNISRAKWNTTLQQIVTELRKQLGNELGNKTIVFQPSSGGDPEI
+>gi|6693886|gb|AAF25018.1| (AF181295) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFTNSAKTIIVQLNVSVEINCTRPNNNTRRGIHIGPGRAFYTTE
+KVIGDIRQAHCNISRAKWNDTLKQIVIKLREQFRNKTIVFNHSSGGDPEI
+>gi|6693888|gb|AAF25019.1| (AF181296) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEGEVVIRSENFTDNAKTIIVQLNTTVKINCTRPSNNTRKSINIGPGRAFYATG
+EVIGNIRQAHCNISRAEWNDTLKLIAAKLREQFGNKTIVFNRSSGGDPEV
+>gi|6693890|gb|AAF25020.1| (AF181297) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPSNNTRTSLTIGPGQVFYRTG
+DIIGDIRQAYCEINGTRWNKVLTQVTEKLKEHFKNKTIIFKPPSGGDLEI
+>gi|6693892|gb|AAF25021.1| (AF181298) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLKEPVEINCTRPNNNTRRSIHIGPGRAFYTTG
+EIIGNIRQAHCNLSRAAWNNTLRQIANKLREQFRNKTIVFNQSSGGDLEI
+>gi|6693894|gb|AAF25022.1| (AF181299) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLNESVVINCTRPNNNTRKSINMGPGRAFYATG
+DIIGDIRQAHCNISRKEWNNTLSKIAEKLREKFNRTIAFNQSSGGDPEI
+>gi|6693896|gb|AAF25023.1| (AF181300) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENISNNAKTIIVHLTESVEINCTRPSNNTRKGIHMGPGGAFYATG
+DIIGDIRQAHCNISGAKWNNTLQQIVIKLREQFKNKTISFNRSSGGDLEI
+>gi|6693898|gb|AAF25024.1| (AF181301) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVIIRSENFTDNVKIMIVQLNKSIEINCTRPSNNTRKGIHIGPGRAFYATG
+SITGDIRQAHCNISRAQWNNTLTQIVGKLREQFKNTTIVFNQTSGGDPEI
+>gi|6693900|gb|AAF25025.1| (AF181302) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSDNFTDNAKTIIVQLNKSIEINCTRPNNNTRKSIHIGPGRAFYTTG
+EIIGDIRQAHCNISRENWHNMLKQVVKKLGEQFVNKTIAFNQSSGGDPEI
+>gi|6693902|gb|AAF25026.1| (AF181303) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEDIVIRSENFTNNAKTIIVQLKESVKIECIRPHNNTRRSIHIAPGRAFYATG
+SIIGDIRQAHCNISLKEWNNTLQQIVTKLREQFGNKTIAFKPSSGGDPEI
+>gi|6693904|gb|AAF25027.1| (AF181304) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVLRSKNFTDNTKTIIVQLKEAVTINCTRPSNNTRKSIPIGPGRAFYTTG
+EIIGDIRQAHCNLSGAEWNKALQQIVTKLREQYKNKTIVFNQSSGGDIEI
+>gi|6693906|gb|AAF25028.1| (AF181305) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLNVSVEINCTRPNNNTRKSISIGPGRAFYATG
+DIIGDIRQAHCNISRAQWNNTLRHIVGKLKVQFKNKTIVFNQSSGGDPEI
+>gi|6693908|gb|AAF25029.1| (AF181306) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLNVSVQINCTRPNNNTRKSINIGPGRAFYATG
+AIIGDIRQAHCNLSRTKWNDTLRQIVVKLREQFGNKTIIFNNSSGGDPEI
+>gi|6693910|gb|AAF25030.1| (AF181307) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVLRSENFTDNAKTIIVQLKEPVQINCTRPNNNTRKSIHIGPGRAFYATG
+DIIGDIRQAHCNLSRASWNDTLKQIVGKLREQFENKTIVFNQSSGGDPQI
+>gi|6693912|gb|AAF25031.1| (AF181308) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFMDNTKTIIVQLKESVEINCIRPNNNTRKSIHIGPGRAFYTTG
+DIIGDIRQAHCNLSSAKWNNTLKQIVDKLREQFGNKTIVFNQSSGGDPEI
+>gi|6693914|gb|AAF25032.1| (AF181309) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSKNFSNNVDTIIVQLNETVEINCTRPNNHTRKSITLGPGKVFYTTG
+DIIGNLRQAYCNISGTKWNNTLRQVANKLREQFENRTIVFTHSSGGDPEV
+>gi|6693916|gb|AAF25033.1| (AF181310) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVIIRSENFTDNTKTIIVQLNETVEINCTRPNNNTRKSIHMGLGRAFYATG
+DIIGDIRQAHCNISKAQWNNTLKQIATKLREHFVNKTIVFNQSSGGDPEI
+>gi|6693918|gb|AAF25034.1| (AF181311) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNETVEINCTRPHNNTRKSIHIGPGRAFYATG
+AITGDIRQAYCNVSRAQWNKTLEKIVDKLRKQFGNGTTIVFNHSSGGDPEI
+>gi|6693920|gb|AAF25035.1| (AF181312) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAQEEVVIRSENITDNAKTIIVQLTKSVNITCARPSNNTRKGIHIGPGRAFYATG
+EITGDIRQAHCNISRAQWNDTLKQIVIKLRKQWNKTIIFTHSSGGDPQI
+>gi|6693922|gb|AAF25036.1| (AF181313) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVMIRSENFTNNVKTLIVQLNETVKINCTKPNNTTRKGIRIGPGRAWWSTT
+GIIGDVRQTHCNISTAKWNNTLKQIVAKLKEQFGNKTIIFNHSSGGDPEI
+>gi|6693924|gb|AAF25037.1| (AF181314) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVMLRSENFTDNTKTIIVQLKEPVVINCTRPNNNTRKSIHIGPGRAFYTTG
+EIIGDIRQAHCNLSRADWNNTLKQIVAKLKEKFENKTIVFNQSSGGDPEI
+>gi|6693926|gb|AAF25038.1| (AF181315) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKVIIVQLNASVEINCTRPNNNTRKSIHIGPGKAFYTTG
+EIVGDIRQAHCNLSRAKWDETLKHIVDKLREQFGNKTIAFNRSSGGDPEI
+>gi|6693928|gb|AAF25039.1| (AF181316) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEGEVVIRSENFTNNAKTIIVHLNQSITINCTRPNNNTRKSIHMGPGRTWYTTG
+DIIGDVRKAHCNLSRVDWNKTLTQIVTKLREQFGNNKTIVFTRHSGGDPEI
+>gi|6693930|gb|AAF25040.1| (AF181317) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTHLLLNGSLAEEEVVIRSENFTDNAKIIIVQLNETVEINCTRPNNNTRKGIHIGPGRAFYATG
+AIIGDIRQAHCNISGVKWEKTLKQVVSKLKEQFGNKTIVFNQSSGGDPEI
+>gi|6693932|gb|AAF25041.1| (AF181318) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFSNNAKTIIVQLKEPVEINCTRPNNNTRKRITMGPGRVYYTTG
+QIIGNIRQAHCNLSRAKWDDTLKQVAVKLREKFGDKTINFTRSSGGDLEI
+>gi|6693934|gb|AAF25042.1| (AF181319) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVMIRSENFTDNVKPIIVQLNTSVNITCVRPNNNTAKSIPIGPGRAFRATG
+RIIGDIRQAHCNISRAQWNKTLGQIVKKLREIKLVGNKTIIFNHSSGGDPEI
+>gi|6693936|gb|AAF25043.1| (AF181320) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNTKTIIVQLNESVVINCTRPNNNTRKGIHIGPGRAFYTTG
+EIIGDIRQAHCNLSSTKWNNTLKQIVKKLREIKQFGNKTIVFNQSSGGDPEI
+>gi|6693938|gb|AAF25044.1| (AF181321) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFSNNAKTIIVQLNESVAINCTRPNNNTRKSIPIGPGRAFYATG
+DIIGNIRQAHCNISRAQWNDTLKLIVEKLGEQFKNKTIIFNHSSGGDPEI
+>gi|6693940|gb|AAF25045.1| (AF181322) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAKEEVVIRSENFTNNAKTIIVQLNKSVEINCTRPNNNTSKSIPIGPGRAFYTTG
+RIIGDIRQAHCNLSRANWNNTLKQIVEKLREQFGNTTTIFFNPSSGGDPEI
+>gi|6693942|gb|AAF25046.1| (AF181323) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLSEGEVIIRSENITNNAKNIIVQLNETVQINCTRPNNNTRKGIHMGPGRAFWATG
+EIVGDIRQAHCNISRTKWNNTLKQIVMKLREQFNKTIIFKTSSGGDPEI
+>gi|6693944|gb|AAF25047.1| (AF181324) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEIVIRSKNFSDNAKIIIVQLNESIQINCTRPNNNTRTSINMGPGRAFWTTG
+DIIGDIRQAHCNISRTQWNKTLHQVAQKLREQFKNKTIVFNHSSGGDPEI
+>gi|6693946|gb|AAF25048.1| (AF181325) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLNESVVINCTRPNNNTRKSIHIGPGRAFYATG
+EIIGDIRQAHCNISRVKWNKTLEQVVGKLREQFKNKTIVFKQSSGGDPEI
+>gi|6693948|gb|AAF25049.1| (AF181326) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFSDNVKTIIVQLNKSIEINCTRPSNNTRRSISIGPGRAFYATD
+RVVGDIRKAHCNLSRTAWNNALKQIATKLMHQFGNKTIVFNQSLGGDPEI
+>gi|6693950|gb|AAF25050.1| (AF181327) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINCTRPYETKRTRTAIGQGQVFYKTG
+DVVGKIGKPYCEINGTKWYEALKQVTGKLKEHFNNKNICFPPPSGGHLEI
+>gi|6693952|gb|AAF25051.1| (AF181328) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSDNITDNAKIIIVQLNETVKINCTRPNNNTRKSIHIGPGRAFFATG
+NIIGDIRQAHCNISGTKWNDTLRKIAIKLRERFGDKTIVFNQSSGGDPEI
+>gi|6693954|gb|AAF25052.1| (AF181329) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVIIRSANLSDNAKTIIVQLKESVEINCTRPNNNTRKSIHIGPGRAFFTTG
+DIIGNIRQAHCNISKTKWNNTLGQIVKKLRENLRNKTIIFNQSSGGDPEI
+>gi|6693956|gb|AAF25053.1| (AF181330) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVMIRSENFSDNARTIIVQLKESVQINCTRPNNNTRKSINIGPGRAFYATG
+EIIGEIRQAHCNITREKWNNTLEQIVIKLRKQFGNKTIVFNQSSGGDPEI
+>gi|6693958|gb|AAF25054.1| (AF181331) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSANFTNNAKTIIVQLKDPVKINCTRPNNNTRKSIHVGPGRALYTTD
+IIGDIRQAHCNISKAEWNNTLQQIVKKLREQFNNKTIIFNQSSGGDPEI
+>gi|6693960|gb|AAF25055.1| (AF181332) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLKDPVKINCTRPNNNTRKSINIGPGRAFYATG
+EIIGDIRRAHCNLSRAAWNNTLKQIVKKLREQFGNKTIVFNQSSGGDPEI
+>gi|6693962|gb|AAF25056.1| (AF181333) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLKEPVEINCTRPNNNTRKSIPMGPGKAFYATG
+DIIGDIRQAYCNINETKWYGALKQIVGKLREQFMNTTIFFHPSSGGDPEI
+>gi|6693964|gb|AAF25057.1| (AF181334) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVMVRSENFTNNAKTIIVQLNETIQINCTRPNNYTRKGIFIGPGRKIYTTG
+NIIGDIRKAHCNISKAAWNNTLKMIAIKLEEQFNKTIVFNQSSGGDPEI
+>gi|6693966|gb|AAF25058.1| (AF181335) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENFTDNAKTIIVQLNETVEINCTRPNNNTRKSIHIGPGRAFYTTG
+EIIGDIRKAYCNISEAKWNNTLRQIVIKLQEQFGNKTIIFNQSSGGDPEI
+>gi|6693968|gb|AAF25059.1| (AF181336) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENLTNNAKIIIVQLNETVKINCTRPNNNTRKSIHVGPGRAFYATG
+AIIGDIRQAHCNVSREKWNNTLYQIVKKLREQFENKTIVFNHSSGGDPEI
+>gi|6693970|gb|AAF25060.1| (AF181337) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEDVIIRSENFTDNAKTIIVQLNESVEINCTRPHNNTRRSIHIGPGRAFYATG
+QIIGDIRQAHCNISRAKWNKTLEQVVKKLREQLGNNKTIAFNQSSGGDPEI
+>gi|6693972|gb|AAF25061.1| (AF181338) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIIIRSVNFTDNAKTIIVQLNESVEITCIRPNNNTRKSIHMGPGKTFYTTG
+DIIGDIRKVYCTINRTEWNNTLQQIVGKLRDFKEVGNKTIIFNQSSGGDPEI
+>gi|6693974|gb|AAF25062.1| (AF181339) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEGVVIRSENITNNAKTLIVQLNETVEINCIRPNNNTRKSIPIGPGRAFYATG
+EVIGDIRQAHCNISTEKWNKTLKQIVTKLREYFPNKTIVFNQSSGGDPEI
+>gi|6693976|gb|AAF25063.1| (AF181340) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSVNFSNNAKTIIVQLNETVEINCTRPNNNTRKSITLGPGRVFYTTG
+QIIGDIRQAHCNISEEKWNNTLKQVVEKLRKQFGENKTIIFKPSSGGDPEV
+>gi|6693978|gb|AAF25064.1| (AF181341) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEGEVIIRSENFTNNAKTIIVQLNETVEINCTRPSNNTRRSITIGPGRAFYATG
+DIIGDIRKAHCNISRVKWENTLKKIATKLEEQFNKSTIIFNQSSGGDPEI
+>gi|6693980|gb|AAF25065.1| (AF181342) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSKNLTDNAKIIIVQLKDPVEINCTRPGNNTRKSIHIGPGRAFYATG
+TITGDIRRAHCNLSIARWNTTLGQVVHKLREQFRNKTIVFKPSSGGDPEI
+>gi|6693982|gb|AAF25066.1| (AF181343) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSENFTNNARIIIVQLNESVLINCSRPSNNTRRSIHIQPGRAFYATG
+EIIGDIRQAHCNVSGTKWNNTLRLIVNKLREQYKNKTIVFNHSSGGDPEI
+>gi|6693984|gb|AAF25067.1| (AF181344) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNESVVINCTRPSNNTRKSIHIGPGRAFYATG
+DIIGDIRQAHCNISRTNWNNTLKKVVNKLREQFGSNTTIVFNQSSGGDPEI
+>gi|6693986|gb|AAF25068.1| (AF181345) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENLTDNAKTIIVQLKEAVEINCTRPNNNTRRRVPLGPGRVWYTTG
+EVIGNIRQAHCNISRAKWNNTLKQVVKKLREHFGNQTIVFNQSSGGDPEI
+>gi|6693988|gb|AAF25069.1| (AF181346) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRTSIHMGLGRSHALTA
+ATVGDIRQAHCNLSWTKWNETLRWIVHNLRKQFKENTTIVFNHSSGGDPEI
+>gi|6693990|gb|AAF25070.1| (AF181347) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEDEVVIRSENFTNNVKTIIVQLNKSVEINCTRPNNNTRKGINMGPGRAFYTTG
+DIIGDIRQAHCNISRVEWNNTLRLIVDKLRKQFNKTIIFNQSSGGDPEI
+>gi|6693992|gb|AAF25071.1| (AF181348) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLNESVVINCTRPNNNTRKSIHIGPGRAFYATG
+QIIGDIRQAHCNISRANWNNTLRQVASKLREHFENKTIIFNQSSGGDPEI
+>gi|6693994|gb|AAF25072.1| (AF181349) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKIIIVQLNDSVEINCTRPNNNTRKSIHIAPGRAFYATG
+EIIGDIRQAHCNISGAKWNNTLKQIVGKLREQFGNKTIVFNQSSGGDPEI
+>gi|6693996|gb|AAF25073.1| (AF181350) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENFTDNTKTIIVQLKEAVEINCTRPNNNTRKSINIGPGRAFYTTG
+DIIGDIRQAYCNISRAKWNDTLKQIADKLREKFGNRTIIFNQSSGGDPEI
+>gi|6693998|gb|AAF25074.1| (AF181351) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFSQNAKTIIVQLKEPVEINCTRPNNNTRKSIHIAPGRAFYATG
+DIIGDIRQAYCNISIAKWNNTLKQIVGKLREQFGNKTTIIFTQSSGGDPEI
+>gi|6694000|gb|AAF25075.1| (AF181352) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNTKTIIVQLNQSVEINCTRPNNNTRRSIHIGPGRAFYATG
+DIIGDIRQAHCNISRVKWNNTLQQIADKLREQFMNKTIIFNQSSGGDPEI
+>gi|6694002|gb|AAF25076.1| (AF181353) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENLTDNAKNIIVQLKESVEINCTRPNNNTRKSITIGPGRAFYTTG
+GIIGDIRQAHCNISRAKWNDTLRQIVDKLRRQFGNKTIVFNPSSGGDPEV
+>gi|6694004|gb|AAF25077.1| (AF181354) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLKEPVQINCTRPGNNTRKSINIGPGRAFYATG
+AIIGDIRQAHCNISIAKWNDTLRQIVVKLREQFKNKTIVFNQSSGGDSEI
+>gi|6694006|gb|AAF25078.1| (AF181355) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSDNFSNNAKIIIVQLNQSVEINCTRPNNNTSQSVRIGPGQSFYATG
+RVIGDIRQAYCILNGSKWNETLRQIALKLRKQFDNKTIAFKPSSGGDPEI
+>gi|6694008|gb|AAF25079.1| (AF181356) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVISTQLLLNGSLAEEDVVIRSKNFSNNAATIIVQLNKTVVINCTRPNNNTRRSIHIGPGSAIYTTG
+EIIGDIRQAHCNLSREDWNNTLKQIVKKLGEQFKNKTIAFNHSSGGDPEI
+>gi|6694010|gb|AAF25080.1| (AF181357) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENFTDNVKTIIVQLNKSVEINCTRPNNNTRKSIHIGPGRAFYATG
+DIIGNIRQAHCNLSRTKWEDTLKQIVTKLGKQFGNNTIVFNQSSGGDPQI
+>gi|6694012|gb|AAF25081.1| (AF181358) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSDNFTDNGKTIIVQLRESVEINCTRPGNNTRKSIPIGPGKAFYATG
+DIIGDIRQAYCEINGTKWKSALSQIVKKLEEQFPNKTITFNQSSGGDPEI
+>gi|6694014|gb|AAF25082.1| (AF181359) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLFNGSLAEEEVVIRSKNFTDNAKTIIVQLNKSVEINCTRPNNNTRKRITLGPGRVFYTTG
+EIIGDIRRAHCNISRAKWNDTLRQIANKLREQFDNKTIIFNQSSGGDPEI
+>gi|6694016|gb|AAF25083.1| (AF181360) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNESVVIDCTRPSNNTRRSITIGPGRAFYTTG
+EVTGDIRQAFCTINGTQWNNTLKLIVAKLNEQFNTTTIVFTQHSGGDPEI
+>gi|6694018|gb|AAF25084.1| (AF181361) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVIIRSENFTNNAKTIIVQLNQSVTINCTRPGNKTIRSFRIGPGKAFYTTR
+EGYIKQAHCNLSRAEWNNTLKQVVKKLGEQFNNTTIIFNHSSGGDPEI
+>gi|6694020|gb|AAF25085.1| (AF181362) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEGVVIRSENFTNNAKTIIVQLNDPVDINCTRPNNNTRKSINIGPGRAFYTTG
+EIIGDIRQAHCNLSIAQWNNTLRQIVHELREQFGNNKTIIFNPSSGGDPEI
+>gi|6694022|gb|AAF25086.1| (AF181363) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEKRVKIRSENISNNDKTIIVQLVKSVKINCTRPSNNTRKSLHMGPGKAFYAMG
+DPIGDIRQAHCNVSRAEWNDTLQQVANQLRKYFGNKTIIFTKSSGGDLEV
+>gi|6694024|gb|AAF25087.1| (AF181364) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSQNFTDNAKTIIVQLKKPVIINCTRPGNNTRKGIHMGPGRAFYTTG
+EIIGDIRQAHCNLSRTDWNNTLGQVVEKLRQQFGNKTVVFNQSSGGDLEI
+>gi|6694026|gb|AAF25088.1| (AF181365) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENLTNNAKTIIVQLNEPVQINCTRPSNNTRKSINIGPGRAFYATG
+AIIGDIRQAHCNVSIAKWNDTLKQIVVKLREQFKNKTIVFNQSSGGDPEI
+>gi|6694028|gb|AAF25089.1| (AF181366) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVLSTQLLLNGSLAEEEVVIRSDNFTDNAKTIIVHLNESVEINCTRPGNNTRKSINIGPGRAFYATG
+QIIGDIRQAHCNISRAKWNKTLEQVVKKLREQFGNKTIVFNQSSGGDPEI
+>gi|6694030|gb|AAF25090.1| (AF181367) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSQNFSNNAKTIIVQLNTTVKINCTRPGNNTRKSIPIGPGRAFYATG
+DIIGDIRKAHCNVSLAQWNNTLKLVVEKLREQFKNKTIVFNQSSGGDPEI
+>gi|6694032|gb|AAF25091.1| (AF181368) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLSEKEVVIRSENFTNNARTIIVQLNESVVINCTRPNNNTRKSIPIGPGRAFYTTG
+EIIGDIRQAHCNLSRTDWNNTLKQIVDKLREQFGKNKTIVFNQSSGGDPEI
+>gi|6694034|gb|AAF25092.1| (AF181369) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTRNEKTIIVHLNESVYINCTRPSNNTRRSIHIAPGKSFYATG
+AIIGDIRQAHCNLSRKEWNKTLGQVVDKLRKQFENKTIIFKPSSGGDPEI
+>gi|6694036|gb|AAF25093.1| (AF181370) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNGKNIIVQLKEAVQINCTRPNNNTRKSIPIGPGRAFYTTG
+DIIGDIRQAHCNISEAKWNDTLRQIANKLGEQFGNNKTIVFNQSSGGDPEI
+>gi|6694038|gb|AAF25094.1| (AF181371) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEDVIIRSANFTDNAKTIIVQLNSSVEINCTRPSNNTRRRIPIGPGRSLVATR
+QISGDIRKAHCNISRTKWNNTLRQVATKLREQFKNKIIAFNNPSGGDPEI
+>gi|6694040|gb|AAF25095.1| (AF181372) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSENITNNAKTIIVHLNESVQINCTRPNNNTRRGIHIGPGRAFYATG
+DIIGDIRQAHCNISRAKWNNTLRQVVDKLRQQFENKTIVFTHSSGGDPEM
+>gi|6694042|gb|AAF25096.1| (AF181373) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFSNNAKTIIVQLNESVEINCTRPNNNTRKSISLGPGRVFYTTG
+QIIGDIRQAHCNISRSKWNDTLKKIVDKLKVQFGNKTIVFNHSSGGDPEI
+>gi|6694044|gb|AAF25097.1| (AF181374) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEREVVIRSENFTNNAKTIIVQLEKPVKINCTRPGNNTRKSIHIGPGRAFYATG
+AITGDIRQAHCNLSKVAWNHTLKQVVHKLREQFGDNKTIIFTPSSGGDPEI
+>gi|6694046|gb|AAF25098.1| (AF181375) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKIIIVQLNESVEINCTRPGNNTRKSIRIGPGGAFYATG
+DIIGDIRQAHCTISTEKWNSTLKKVVTVLKEQFGNKTIIFKQPAGGDPEI
+>gi|6694048|gb|AAF25099.1| (AF181376) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFSQNAYTIIVQLNKSVIINCTRPSNNTRKGIHIGPGRAFYTTG
+QIIGDIRQAHCNLSKTDWNNTLQQIVRKLRLEYENKTIEFKPSSGGDPEI
+>gi|6694050|gb|AAF25100.1| (AF181377) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRAFYTTG
+AIIGDIRQAHCNLSRTRWNDTLKHIVNKLRGQFGNKTIVFTQSSGGDPEI
+>gi|6694052|gb|AAF25101.1| (AF181378) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNESIQINCIRPNNNTRKSIHIGPGRAFYATG
+DIIGEIRQAHCNLSKANWNNTLKQIVTKLREQFGNKTIVFNPSSGGDPRI
+>gi|6694054|gb|AAF25102.1| (AF181379) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKSIIVQLNKPVEINCTRPNNNTRKSIHIGPGRAFYATG
+EIIGDIRQAHCNLSRANWNETLKQIATKLRKQFGNKTIIFNQSSGGDPEI
+>gi|6694056|gb|AAF25103.1| (AF181380) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEKEVVIRSENFTNNAKTIIVQLKDAVEINCTRPNNNTRKSISMGPGRVFYTTG
+EVIGNIRQAHCNLSREKWNDTLTQIVTKLGEQFGNKTIVFNSSSGGDLEI
+>gi|6694058|gb|AAF25104.1| (AF181381) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEGDVMIRSENLTNNAKTIIVQFNETVKINCTRPNNNTRTSIRIGPGQAFYATG
+EIIGDIRKAHCNVSRTDWNEALRKVAEKLRQHFNNTNISFTKPSGGDLEI
+>gi|6694060|gb|AAF25105.1| (AF181382) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEGEEVVIRSENFTNNAKTIIVQLKDPVEINCTRPNNNTRKSIHIAPGSAFFAT
+GDIIGDIRQAHCNISREKWNETLKQIVVKLRKQFENKTIVFNQPSGGDPEI
+>gi|6694062|gb|AAF25106.1| (AF181383) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNQSVGIHCERPNNNTRKSITIGPGRAFYTTG
+GIIGNIRQAHCNISEADWNNTLKKIVGKLREYFGNKTIVFNQSSGGDPEI
+>gi|6694064|gb|AAF25107.1| (AF181384) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEPVQINCTRPNNNTRKRISLSPGRVFYTTG
+EIIGNIRQAHCNLSRTQWNKTLGEIAMKLREHFKNKTIAFNPSSGGDPEI
+>gi|6694066|gb|AAF25108.1| (AF181385) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEDIVIRSENLTNNAKSIILQLNKSVEINCTRPNNNTRKGIHIGPGRAFYATG
+HIIGDIRQAHCNISKKDWDDTLKQIATKLRETFKNKTIAFNQSSGGDPEI
+>gi|6694068|gb|AAF25109.1| (AF181386) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVEIRSDNFSDNAKTIIVQLKEYVEINCTRPHNNTRKSIHMGPGRAFYTTG
+EIIGDIRQAHCNLSRAKWNNTLKQIAKKLGEQFQNKTIIFNQSSGGDPEI
+>gi|6694070|gb|AAF25110.1| (AF181387) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVLSTQLLLNGSLAEGEVMIRSENFTNNAKSILVQLNETVEINCTRPNNNTRKSIYVGPGRAFYATG
+QIIGDIRQAHCNLSRAKWNETLKQIVTKLREKFGNKTIIFNQSSGGDPEL
+>gi|6694072|gb|AAF25111.1| (AF181388) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKGVVIRSVNFSDNAKTIIVQLNESVQINCTRPNNNTRRSIHLGPGRAFYTTG
+NIIGDIRKAYCNINGTKWNNTLKQIVIKLRREFGSNTIVFNQSSGGDPEI
+>gi|6694074|gb|AAF25112.1| (AF181389) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSENFTNNAKTIIVQLNETVEINCTRPNNNTRKRIHIGPGRAFYATG
+QIIGNIRQAHCNLSSAKWNETLKRIATKLREQFGNNTTIFFKPSSGGDPDI
+>gi|6694076|gb|AAF25113.1| (AF181390) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSENFTDNAKTIIVQLNKSIEINCTRPHNNTRKSIPMGPGKAFYTTG
+DIIGDIRQAHCNLSRAEWNDTLRQIVDKLKEQFGNNKTIVFNQSSGGDPEI
+>gi|6694078|gb|AAF25114.1| (AF181391) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSANFTDNAKSIIVQLNETVKINCTRPGNNTRKSIHIGPGRAFYATG
+DIIGDIRQAHCNISRAQWNNTLKQIVEKLREQFGNKTIVFNHSSGGDPEI
+>gi|6694080|gb|AAF25115.1| (AF181392) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLNESVVINCTRPNNNTRRSIHMGPGGAFYATG
+DIIGNIRQAHCNLSRAQWNDTLEQIVNKLKEQFNNTTIIFDPSSGGDPEI
+>gi|6694082|gb|AAF25116.1| (AF181393) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSANFTDNTKTIIVQLNQSVQINCTRPNNNTRESIPMGPGTAFYTTG
+AIIGDIRQAHCNLTRAKWNDTLQQIVGKLREQFGNQTIVFNQSSGGDPEI
+>gi|6694084|gb|AAF25117.1| (AF181394) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNTKTIIVHLNESVEINCTRPNNNTRKSIHIGPGRAFYATG
+DIIGDIRQAHCNISEAKWNKTLQHIVNKLREQFGNKTLAFNQSSGGDPEI
+>gi|6694086|gb|AAF25118.1| (AF181395) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENITDNAKTIIVQLNNSVEINCTRPNNNTRKSMPIGPGRAFYATG
+DIIGDIRQAYCSINGTQWNNTLKHVVDKLKEQFNKTIVFNQSSGGDPEI
+>gi|6694088|gb|AAF25119.1| (AF181396) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENLTDNTKTIIVQLKEAVVINCTRPNNNTRKSIPIGPGKAFYTTG
+DIIGDVGQAHCNLSGTEWNDTLRQIVDKLREQFENKTIVFNQSSGGDPEI
+>gi|6694090|gb|AAF25120.1| (AF181397) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLKESVEINCTRPNNNTRKSVPIGPGRAFYATG
+DIIGDIRQAYCNISEAKWNDTLRQIVNKLREQFKNKTIVFNQSSGGDPEI
+>gi|6694092|gb|AAF25121.1| (AF181398) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIIQLKESVIINCTRPNNNTRKSIPIGPGRAFYATG
+DIIGDIRQAHCNLSRAQWNNTLKQIVQKLREQFENRTIVFNQSSGGDPEI
+>gi|6694094|gb|AAF25122.1| (AF181399) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENITNNAKTIIVQLNVSVEINCTRPNNNTRKSIPIGPGRVFFTGE
+IIGNIRQAHCNLSRSKWENTLKQVAIKLREKFGNNKTIFFHPSSGGDPEI
+>gi|6694096|gb|AAF25123.1| (AF181400) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEDIVIRSENFTNNAKTIIVQLKVPVQINCTRPNNNTRRSINLGPGRAFYATG
+QIIGDIRQAHCNISRAQWNDTLKEIVKKLGEQFKDKTIAFNKSSGGDPEI
+>gi|6694098|gb|AAF25124.1| (AF181401) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEDIVIRSENFTNNAKTIIVQLNEAVNITCIRPHNNTRKSIPMGPGRAWYATG
+DIIGDIRQAHCIITRADWNNTLNQTVSKLREQFGNNKTIVFRPSSGGDPEI
+>gi|6694100|gb|AAF25125.1| (AF181402) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSANFSDNTKTIIVQLKEPVEINCTRPNNNTRKSINIGPGRAFYATG
+DIIGDIRQAHCNISRTTWNNTLKQIVGKLREQFGNKTIIFNPSAGGDPEI
+>gi|6694102|gb|AAF25126.1| (AF181403) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFSDNAKTIIVQLKEPVEINCTRPNNNTRRSITIGPGSAFYTGD
+IIGDIRQAHCNLSIAKWNDTLIQIVDKLREQFGNKTIVFNQSSGGDPEI
+>gi|6694104|gb|AAF25127.1| (AF181404) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSVNLTDNTKTIIVQLNESIEIDCTRPSNNTRKGIHIGPGRAFYTTG
+EITGDIRQAHCNLSRAKWEDTLEQIAKKLRKQLGNKTIVFNQSSGGDPEI
+>gi|6694106|gb|AAF25128.1| (AF181405) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAKEEIVIRSENLTDNAKTIIVHLNESVEINCTRPNNNTRKGIHIGPGKAFYATG
+EIIGDIRQAHCNISGTKWNNTLKQVVIKLREKFGKNKTIVFNQSSGGDPEI
+>gi|6694108|gb|AAF25129.1| (AF181406) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSKNFSNNAKTIIVQLNASVVINCTRFNNNTRKSIHIGPGGAFYATG
+DIIGDIRQAHCNLSRAKWNETLKHIVVKLREQFNTTIVFNPSSGGDPEI
+>gi|6694110|gb|AAF25130.1| (AF181407) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVIIRSENFTDNTKTIIVQLKEPVEINCTRPNNNTRNSIHIGPGRAFYTTG
+DIIGDIRQAHCNLSITKWNNTLKQIADKLREQFENKTIVFNPSSGGDPEI
+>gi|6694112|gb|AAF25131.1| (AF181408) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNESVQINCTRPSNNTRKGIHIGPGRAFYTTG
+DIIGDIRQAHCNLSRANWNNTLKQIVKKLREQFPNKTIIFKQSSGGDPEI
+>gi|6694114|gb|AAF25132.1| (AF181409) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSKNFTDNAKTIIVQLNEPVIINCTRPNNNTRKGIHIGPGGAFYTTG
+EIIGDIRQAHCNLSIAQWNNTLKQIVDKLGEQFKNKTIVFNQSSGGDPEI
+>gi|6694116|gb|AAF25133.1| (AF181410) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLKESIEINCTRPSNNTRKGIHIGPGSVFYTQE
+ITGDIRQAHCNISRAKWNNTLKQIVKKLREKFENKTIVFNQSSGGDPEI
+>gi|6694118|gb|AAF25134.1| (AF181411) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLKESVQINCTRPNNNTRKSIHIGPGRAFYTTG
+AIIGDIRQAHCNISRAKWNDTLKQVVNKLREQFKNKTIVFKNSSGGDPKI
+>gi|6694120|gb|AAF25135.1| (AF181412) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSIAEGDIVIRSDNITNNAKTIIVQLNDTVVINCTRPNNNTRKSIHIGPGRAFYATG
+DIIGDIRQAHCNISRTKWNNILKQIAEKLREQFVNKTIVFNQSSGGDPEV
+>gi|6694122|gb|AAF25136.1| (AF181413) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEGIVIRSENITNNAKTIIVQLAKPVRINCTRPNNNTRRSVRIGPGQTFYATG
+DIIGDIRQAYCQVNRTEWNSTLQEVAAQLKKYFKNTTIILFNKSSGGDLEI
+>gi|6694124|gb|AAF25137.1| (AF181414) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSVNFTDNAKTIIVQLNESVVINCTRPNNNTRKSINIGPGRAFYATG
+EIIGNIRQAHCNLSRTEWNNTLKQVVDKLREKFGNNKTIVFNQSSGGDPEI
+>gi|6694126|gb|AAF25138.1| (AF181415) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSDNFTDNAKIIIVQLNETVEINCTRPNNNTRRSISIGPGRAFYATG
+DIIGDIRQAHCNISGAKWNNTLKQIAIKLREQFENKTIVFNPSSGGDPEI
+>gi|6694128|gb|AAF25139.1| (AF181416) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKIIIVQLKESVQINCTRPNNNTRKSIHMGPGKVLYTTG
+DIIGDIRQAYCNLSRAKWNDTLRQIAIKLKEQFKNKTIIFNQSSGGDPEI
+>gi|6694130|gb|AAF25140.1| (AF181417) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIIIRSENLTNNAKIIIVQLNESVTIECTRPYNNTRQSTRIGPGQAIYTTN
+IIGDIRQAHCNISEKAWNKTLQQVAKKLRDLLNTTTIIFKPSSGGDPEI
+>gi|6694132|gb|AAF25141.1| (AF181418) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEKVAIRSENITNNAKTIIVQFVEPVKINCSRPSNNTRKSVRIGPGQTFYATG
+EIIGDIRQAHCNVSEAAWNRTLQQVATQLGNYFENKTINFTKPSGGDLEI
+>gi|6694134|gb|AAF25142.1| (AF181419) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNAKTIIVQLNESVEINCTRPNNNTRRSIHIGPGAFYTTGE
+IIGDIRQAHCNISGAKWNDTLKQIVGKLKEQFGNKTIFFNQSSGGDPKI
+>gi|6694136|gb|AAF25143.1| (AF181420) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSANFTDNAKIIIVQLNESVAINCIRPNNNTRKSIPIGPGKAFYTTG
+EIIGDIRQAHCNLSKAEWNNTLRQIAIKLREHFKNKTIIFNQSSGGDPEI
+>gi|6694138|gb|AAF25144.1| (AF181421) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEGVVIRSENFTDNAKTIIVQLDQFVKINCTRPNNNTRKSINIGPGRAFYTTG
+AIIGDIRQAHCNISRTEWNNTLKKVVAKLREQFRNKTIVFNQPSGGDPEI
+>gi|6694140|gb|AAF25145.1| (AF181422) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTHLLLNGSLAEEDVVIRSKNITDNTKIIIVQLNKSVEINCTRPNNNTRRSIPIGPGRAFYATG
+GIIGDIRQAHCNISRAEWNNTLRQIVDKLREQFENKTIIFNQSSGGDPEV
+>gi|6694142|gb|AAF25146.1| (AF181423) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTENTKTIIVQLNKSVEINCTRPNKNVRHRIHIGPGRAFYTAK
+AIIGDIRQAHCNLSRADWNDTLKLIVDKLREQFKNKTIAFNPHAGGDPEI
+>gi|6694144|gb|AAF25147.1| (AF181424) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLNESVKINCTRPNNNTRKGIHLGPGGAFYATG
+AIIGNIRQAHCNISGTKWNATLKQIVAKLQDQYGDNKTIIFQPSSGGDPQI
+>gi|6694146|gb|AAF25148.1| (AF181425) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVHLNESVEINCARPNNNTRKSIHIGPGRAFYATG
+NIIGNIRQAYCNISGAKWNDTLRQIAKKLREQFNRTIVFNQSSGGDLEI
+>gi|6694148|gb|AAF25149.1| (AF181426) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEDEVVIRSENFTNNAKTILVQLSQSVKINCTRPGNNTRKSIHMGPGKAFYATG
+DIIGDVRQAHCNISGKAWNETLKQVVAKLREQFRNKTIIFQPSSGGDPEI
+>gi|6694150|gb|AAF25150.1| (AF181427) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNVKTIIVQLKEPVVINCTRPNNNTRKSINIGPGRAFYTTG
+QIIGDIRQAHCNISEAKWNETLKQIAQKLREQFENKTISFNQSSGGEFSI
+>gi|6694152|gb|AAF25151.1| (AF181428) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSDNFTNNAKIIIVQLNESVEINCTRPNNNTRKRISLGPGRVFYTTG
+EIIGDIRQAHCNVSRTKWNNILGQIVIKLREQFGNKTIVFNQSSGGDLEI
+>gi|6694154|gb|AAF25152.1| (AF181429) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENFTDNAKTIIVQLKNPVVINCTRPNNNTRKSIHIGPGRAFYTTG
+DIIGDIRQAHCNLSRSEWNNTLTQIVSKLREQFGNKTIVFNRSSGGDPEI
+>gi|6694156|gb|AAF25153.1| (AF181430) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSDNITDNTKTIIVQLKEPVEINCTRPNNNTRKSIHIGPGRAFYASG
+EIIGDIRQAHCNVSEAKWNNTLKQIAKILREKFNNKTIVFNQSSGGDPEI
+>gi|6694158|gb|AAF25154.1| (AF181431) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSENFTNNAKTIIVQLNDSVVINCTRPNNNTRKGIHIGPGRAFYTTG
+DIIGDIRQAHCNLSRSAWNNTLKQIVLKLREQFGNKTIVFNRSSGGDPEI
+>gi|6694160|gb|AAF25155.1| (AF181432) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTDNTKNIIVQLNVTVQINCTRPNNNTRKSITIGPGRAFFATG
+DIIGDIRQAHCNISREKWNNTLQQIVIKLREQFGNNKTIVFNHSSGGDPEI
+>gi|6694162|gb|AAF25156.1| (AF181433) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSDNFTDNAKTIIVQLNKSVEINCTRPNNNTRKSIHIGPGRAFYATD
+IIGNIRQAHCNISGVEWNNTLKQIVEKLGEQFGNKTIVFNQSSGGDPEI
+>gi|6694164|gb|AAF25157.1| (AF181434) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEGVVIRSENFTNNVKTIIVQLNESVAINCTRPNNNTRKSISIGPGRAFYATG
+DIIGDIRKAHCNLSRAQWNNTLNQIVTKLQEQYGKNKTIIFNPSSGGDPEI
+>gi|6694166|gb|AAF25158.1| (AF181435) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTHLLLNGSLAKEEVVIRSSNFTDNAKIIIVQLNTAVEVNCTRPNNNTRKSISMGPGRAFYTTG
+DIIGDIRQAHCNISEGKWMDTLKKVATKLRGQFENKTIVFKQSSGGDPEI
+>gi|6694168|gb|AAF25159.1| (AF181436) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNVKIIIVQLNESVEINCTRPNNNTRKSIPIGPGRAFYTTG
+DIIGDIRQAHCNLSMAKWNSTLKQVVEKLREQFGNNKTIVFNQSSGGDPEI
+>gi|6694170|gb|AAF25160.1| (AF181437) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNETVEINCTRPNNNTRKSIHMGWGRAFYATG
+EIIGNIRQAYCTINGTKWNNTLKQVVRKLKEQFNTTTINFTQSSGGDPEI
+>gi|6694172|gb|AAF25161.1| (AF181438) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEKEVVIRSENFTNNAKIIIVQLNSSVEINCTRPNNNTRKSIHIAPGRAFYATG
+DIIGDIRQAHCNLSRTKWEDTLKQIAKKLREQFKNKTIIFNQSSGGDPEI
+>gi|6694174|gb|AAF25162.1| (AF181439) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEGEVVIRSENFTNNAKTIIVQLNESIAIECIRPNNNTRKSIHVGPGKALYTTG
+VIGDIRQAYCNLNRTKWNDTLKQIVTKLKEQFGGKPIVFNQSSGGDPEI
+>gi|6694176|gb|AAF25163.1| (AF181440) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEVVIRSEQFSDNAKTIIVQLNESVEINCTRPNNNTRRSISMGPGKAIYTTG
+AIIGNIRQAYCNISITKWNNTLKQIVHKLREQFGENKTINFTQPSGGDPEI
+>gi|6694178|gb|AAF25164.1| (AF181441) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEEEIVIRSENFTNNAKTIIVQLNESVVINCTRPNNNTRKSIHLGPGGTFYATG
+KIIGDIRRAQCNINRAKWNNTLKQIVKKLKELFNNKTIIFNESSGGDAEI
+>gi|6694180|gb|AAF25165.1| (AF181442) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVIIRSSNFTNNAKVIIVQLNESVEINCTRPNNNTRKSITMGPGRVFYSTG
+QIVGDIRQAHCNLSRAKWNDTLRQITIKLREQFKNKTIIFNQSSGGDPEI
+>gi|6694182|gb|AAF25166.1| (AF181443) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSENFTNNAKTIIVQLKNPVEINCTRPNNNTRKSIQVGPGKALYTTG
+AIIGDIRQAHCNLSRTTWNETLGQIVSKLREQFKNRTIVFNQSSGGDPEI
+>gi|6694184|gb|AAF25167.1| (AF181444) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIKPVVSTQLLLNGSLAEQEVVIRSANFSDNAKTIIVQLKKSVEIECIRPNNNTRKGIHMGPGKAIYTTG
+EIIGDIRQAHCNLSRADWNNTLKQIVIKLREQFENKTIIFNQSSGGDPEI
+>gi|6694186|gb|AAF25168.1| (AF181445) envelope glycoprotein [Human immunodeficiency virus type 1]
+GIRPVVSTQLLLNGSLAEEEVVIRSANFTDNAKTIIVQLNQSVEIHCMRPNNNTRKSIHIAPGRAFYTTG
+NIIGDIRQAHCNISEPQWNNTLRLIVTKLREQFRNKTIVFNQSSGGDPEI
+>gi|6694188|gb|AAF25169.1|AF182341_1 (AF182341) NADH dehydrogenase [Buergersiochloa bambusoides]
+WVIPLLPLLVIMSMGFGLILIPTATKNLRRIWAFPSVLLLSIAMVFSVYLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARLFPLFIPLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLCGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFKNYSNTKEGSLYSISLWGKRVPKGVNRDFILSTTKS
+GVFFSQNISKIHGNTRNRIGSFSISFGAKNTFVYPHETGNTMLFPLFILLLLTLFIGSIGIHFDDVVMDN
+GIAELTILSKWLTPSINFFQESSNSSINSYEFFTNAISSVSLAMFGLFIAYIFYGSAYSFFHNLDLINSL
+VKKSPKKSFLDQVKKKIYSWSYNRGYIDIFYTRFFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIGE
+G
+>gi|6694190|gb|AAF25170.1|AF182342_1 (AF182342) NADH dehydrogenase [Shibataea kumasaca]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPCVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAATMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSIIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTRNRIGSFSTSFGAKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMD
+NGIAELTILSKWLTPSINFFQESSNSSINSYEFITNAISSVSLAMFGLSIAYIFYGSAYSFFQNLDLINS
+LVKESPKKFFSDQVKKKIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EGIKY
+>gi|6694192|gb|AAF25171.1|AF182343_1 (AF182343) NADH dehydrogenase [Sucrea maculata]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPCVLFLSIAMVFSVYLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGISSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAATMVAAGIFLLARLFPLFISLP
+LIMSFVSLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSLIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVRFQNYSNTKQSSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIQGNTRNRIGSFSISFGAKNTFVYPHETGNTMLFPLFILLLLTLFIGSIGIHFDNNNGV
+MDNEIAELTILSKWLTPSINFFQKSSNSSINSYEFFINAISSVSLAMFGLFIAYIFYGSAYSFFQNLDLI
+NFLVKKSPKKTFSDQVKKKIYSWSYNRGYIDIFYTRLFTLGIRRLTELTQFFDKGVIDGITNGVGLAGFC
+IGEG
+>gi|6694194|gb|AAF25172.1|AF182344_1 (AF182344) NADH dehydrogenase [Sasa variegata]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPCVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSIIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTRNRIGSFSTSFGAKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMD
+NGITELTILSKWLTPSINFFQESSNSSINSYEFITNAISSVSLAMFGLSIAYIFYGSAYSFFQNLDLINS
+LVKESPKKFFSDQVKKKIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694196|gb|AAF25173.1|AF182345_1 (AF182345) NADH dehydrogenase [Puelia olyriformis]
+WVIPLLPLPVIMSMGFGLFLIPTATKNLRRIWVFPSVLFLSIAMVFSVHLSIQQINGSSIYQYLWSWTIN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNISMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLFTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAATMVAAGIFLLARLLPLFISLP
+FIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVFMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSRLYS
+PFFGIIASFTAGLTAFYMFRVYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFVLSTTKS
+GVSFFSQNISKIHGNTRSRIGSFSTSFGAKNTSVYPHETGNTMLFPLLILLLFTLFIGSIGIHFDNGVMD
+NGVVELTILSKWLTPSINFFQESSNSSINSYEFITNATSSVSLAIFGLFIAYIFYGSAYSFFQNLDLINL
+INFLVKGNPKKSFLDQVKKRIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGIIDGITNGVGLAGF
+CIGEG
+>gi|6694198|gb|AAF25174.1|AF182346_1 (AF182346) NADH dehydrogenase [Yushania exilis]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPCVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSIIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNRSKIHGNTRNRIGSFSTSFGAKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMD
+NGIAELTILSKWLTPSINFFQESSNSSINSYEFITNAISSVSLAMFGLSIAYIFYGSAYSFFQNLDLINS
+LVKEGPKKFFSDQVKKKIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694200|gb|AAF25175.1|AF182347_1 (AF182347) NADH dehydrogenase [Alvimia gracilis]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLLLSIAMVFSVHLSVQQINGSSIYQYLWSWTIN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHETXMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSIIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRSTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTKNRIGSFSTSFGAKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMN
+NGIAELTILSKWLTPSINFFQESSNSSINFYEFITNAISSVSLAMFGLFIAYIFYGSAYSFFQNLDLINS
+LVKESPKKYFLDQVKKKIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+E
+>gi|6694202|gb|AAF25176.1|AF182348_1 (AF182348) NADH dehydrogenase [Melocanna baccifera]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTRNRIGSFSTSFGVKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMD
+NGIAELTILSKWLTPSISFFQESSNSSINSYEFITNAISSVSLAMFGLFIAYIFYGSAYSFFQNFYLINS
+LVKESPKKSFLDQVKKKIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694204|gb|AAF25177.1|AF182349_1 (AF182349) NADH dehydrogenase [Rhipidocladum pittieri]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLFLSIAMVFSVHLSVQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFIYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHEAXMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSIIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRSTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGLLYSISLWGKRKPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTRNRIESFSTSFGAKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMN
+NGIAELTILSKWLTPSINFFQESSNSSINSYEFLANAISSVSLAMFGLFIAYIFYGSAYSFFQNLDLINS
+LVKESPKKYFLDQVKKKIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694206|gb|AAF25178.1|AF182350_1 (AF182350) NADH dehydrogenase [Otatea acuminata]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+SGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHATXMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRSTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTRNRIGSFSTSFGAKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMD
+KGIAELTILSKWLTPSINFFQESSNSSINSYEFITNAISSVSLAMFGLFIAYIFYGSAYSFFQNLDLINF
+LVKESPKKSFLDQVKKKIYSWSYNRGYIDIFYTKVFTLGIRGLTELTQFFDKGVIDGITNGVGLTGFCIG
+EG
+>gi|6694208|gb|AAF25179.1|AF182351_1 (AF182351) NADH dehydrogenase [Hickelia madagascariensis]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHEATMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGAPLALAQRDIKKSLAYSTMSQLGYMMLALGIGSSQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTRNRIGSFSTSFGVKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGILFDNGVMD
+NGIAELTILSKWLTPSISFFQESSNSSMNSYEFITNAISSVSLAMFGLFIAYIFYGSAYSFFQNLYLINS
+LVKESPKKYFLDQVKKKIYSWSYNRGYIDIFYTRVFILGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EGIK
+>gi|6694210|gb|AAF25180.1|AF182352_1 (AF182352) NADH dehydrogenase [Nastus elatus]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARFLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSSTKEGSLYSISLWGKRIPKGVNRDFILSTTKS
+GVSFFSQNISKIHGNTRNRIGSFSNSFGVKNPFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMD
+NGIAELTILSKWLTPSISFFQESSNSSINSYEFITNAISSVSLAMFGLFIAYIFYGSAYSFFQNLYLINS
+LVKESPKKSFLDQVKKKIYSWSYNRGYIDIFYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694212|gb|AAF25181.1|AF182353_1 (AF182353) NADH dehydrogenase [Eremitis sp. Clark and Zhang 1343]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLFLSIAMVFSVYLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSYDEGYLRFFVYISFFNTSMLGLVTSSNFIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARLFPLFISLP
+LIMIFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYIPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFAAGLTAFYMFRIYLLTFDGYLRVHFQNYSNTKEGSLYSISLWGKRIPQEVNRDFIVSTTKS
+GVSFFSQTISKMQGNTRNRIGSFSTSFGTKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMD
+NGIAELTILSKWLTPSINFFQESSNSSINSYEFLTNAISSVSLAMFGLFIAYIFYGSTYSFFQNLYLINS
+LLKKSPKNTFLDQVKKKIYSWSYNRGYIDIFYTRFFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694214|gb|AAF25182.1|AF182354_1 (AF182354) NADH dehydrogenase [Pariana radiciflora]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLFLSIAMVFSVYLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSYDEGYLRFFVYISFFNTSMLGLVISSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRIGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGINSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARLFPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGIGSYQAALFHLITHAYSKALLFL
+GSGSVIHSMEPLVGYSPDKSQNMVLMGGLRKYIPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PFFGIIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSNTKEGSLYSISLWGKRIPQEVNRDFILSTTKS
+GVSFFSQNISKMQGNTRNRIGSFSTSFGAKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGLHFDNGVMD
+NGIAELTVLSKWLTPSINFFQESSNSSINSYEFLTNAISSVSLAMFGLFIAYIFYGSAYSFFQNLYLKNS
+LLKKSPKKTFLDQVKKKIYSWSYNRGYIDIFYTRFFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694216|gb|AAF25183.1|AF182355_1 (AF182355) NADH dehydrogenase [Neurolepis aperta]
+WVIPLLPLPVIMSMGFGLILIPTATKNLRRIWAFPSVLLLSIAMVFSVHLSIQQINGSSIYQYLWSWTVN
+NDFSLEFGYLIDPLTSIMLILITTVGILVLIYSDDYMSHDEGYLRFFVYISFFNTSMLGLVTSSNLIQIY
+FFWELVGMCSYLLIGFWFTRPIAASACQKAFVTNRVGDFGLLLGILGFFWITGSLEFRDLFKIANNWIPN
+NGMNSLLTTLCAFLLFLGAVAKSAQFPLHVWLPDAMEGPTPISALIHAAXMVAAGIFLLARLLPLFISLP
+LIMSFISLVGTITLFLGATLALAQRDIKRSLAYSTMSQLGYMMLALGVGSYQAALFHLITHAYSKALLFL
+GSGSIIHSMEPLVGYSPDKSQNMVLMGGLRKYVPITRTTFLWGTLSLCGIPPLACFWSKDEILSNSWLYS
+PYFGVIASFTAGLTAFYMFRIYLLTFDGYLRVHFQNYSNTKEGSLYSISLWGKRIPKGVNRNFILSTTKS
+GVSFFSQNISKIHGNTRNRIGSFSTSFGTKNTFVYPHETGNTMLFPLFILLLFTLFIGSIGIHFDNGVMG
+NGIAELTILSKWLTPSINFFQESSNSSINSYEFITNAIYSVSLAMFGLFIAYIFYGSAYSFFQNLDLINS
+LVKESPKKYFFDQVKKNIYSWSYNRGYIDILYTRVFTLGIRGLTELTQFFDKGVIDGITNGVGLAGFCIG
+EG
+>gi|6694218|gb|AAF25184.1|AF182402_1 (AF182402) metalloregulator RmtA [Streptococcus gordonii]
+MTPNKEDYLKCLYELGTRHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKKAGYLLTDLGLKLVS
+DLYRKHRLIEVFLVHHLGYTTEEIHEEAEVLEHTVSDHFVERLDQLLDYPKACPHGGTIPAKGELLVEKH
+KLTLEEAKEKGDYILARVHDNFDLLTYLERNGLQVGKTIRFLGYDDFSHLYSLEVDGQEIQLAQPIAQQI
+YVEKI
+>gi|6694219|gb|AAF25185.1|AF182402_2 (AF182402) unknown [Streptococcus gordonii]
+MKQLDFNSIYKNDSQQSTGLLFIRAYHKWHGLIKSQLKTIDLTHPQFVLLTTLAALLRQQEWVSQTDIAR
+FSDMDVMTV
+>gi|6694221|gb|AAF25186.1|AF182949_1 (AF182949) voltage-gated sodium channel subunit beta1-A [Rattus norvegicus]
+MGTLLALVVGAVLVSSAWGGCVEVDSETEAVYGMTFKILCISCKRRSETTAETFTEWTFRQKGTEEFVKI
+LRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYECHVYRLLFFDNYEHNTSVVK
+KIHLEVVDKGKWSLVTLWQARWRDRWKEGDRLVSHRGQLTPRSHRGKDTPFLVLETSALQHTGGQIRTPT
+PPPTNGMCIGLHSCCVTSDGCIPISEPQACPQGPERIFCMACCVSQAGPHWRDVGTYLRPQWE
+>gi|6694223|gb|AAF25187.1|AF184244_1 (AF184244) ribonucleoprotein [Danio rerio]
+MSNGYEDHMADELIDSKTNLIVNYLPQNMSQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVNPN
+DAERAISTLNGLRLQSKTIKVSYARPSSDSIKDANLYISGLPKTMTQKDVEEMFGRYGRIINSRVLVDQA
+SGLSRGVAFIRFDKRAEAEDAIKDLNGQKPPGAAEQMTVKFAASPNQVKNTQVIPQVYHQQSRRFGGPVH
+HQAQRFRFSPMSVDHMSGMSGVNVPGNSSSGWCIFIYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTN
+KCKGFGFVTMTHYEEAAMAIASLNGYRLGDKILQVSFKTSKSHK
+>gi|6694225|gb|AAF25188.1|AF184245_1 (AF184245) ribonucleoprotein [Danio rerio]
+MPNGYEDPMGDEPSDAKTNLIINYLPQNMSQEELRSLFSSIGEVESAKLIRDKMAGHSLGYGFVNYVNPS
+DAERAINTLNGLRLQSKTIKVSYARPSSDGIKDANLYISGLPKTMTQKNVEDMFTQYGRIINSRILVDQA
+SGLSRGVAFIRFDKRSEAEEAIKDLNGSKPSGASEPITVKFAANPNQSKNSQLLSQLYHTQSRRFGGPVH
+HQPQRFRFSPMSVDHSVSSMNVASSSSSGWCIFVYNLGQDADEGILWQMFGPFGAVTNVKVIRDFNTSKC
+KGFGFVTMTNYEEAAMAISSLNGYRLGDKVLQVSFKSSKSHK
+>gi|6694227|gb|AAF25189.1|AF187147_1 (AF187147) drebrin A [Mus musculus]
+MAGVSFSGHRLELLAAYEEVIREESAADWALYTYEDGSDDLKLAASGEGGLQELSGHFENQKVMYGFCSV
+KDSQAALPTYVLINWVGEDVPDARKCACASHVAKVAEFFQGVDVIVNASSVEDIDAGAIGQRLSNGLARL
+SSPVLHRLRLREDENAEPVGTTYQKTDAAVEMKRINREQFWEQAKKEEELRKEEERKKALDARLRFEQER
+MEQERQEQEERERRYREREQQIEEHRRKQQSLEAEEAKRRLKEQSIFGDQRDEEEESQMKKSESEVEEAA
+AIIAQRPDNPREFFRQQERVASASGGSCDAPAPAPFNHRPGRPYCPFIKASDSGPSSSSSSSSSPPRTPF
+PYITCHRTPNLSSSLPCSHLDSHRRMAPTPIPTRSPSDSSTASTPIAEQIERALDEVTSSQPPPPPPPPP
+PTQEAQETTPSLDEELSKEAKVTAAPEVWAGCAAEPPQAQEPPLLQSSPLEDSMCTESPEQAALAAPAEP
+AASVTSVADVHAADTIETTTATTDTTIANNVTPAAASLIDLWPGNGEEASTLQAEPRVPTPPSGAEASLA
+EVPLLNEAAQEPLPPVGEGCANLLNFDELPEPPATFCDPEEEVGETLAASQVLTMPSALEEVDQVLEQEL
+EPEPHLLTNGETTQKEGTQASEGYFSQSQEEEFAQSEEPCAKVPPPVFYNKPPEIDITCWDADPVPEEEE
+GFEGGD
+>gi|6694229|gb|AAF25190.1|AF187148_1 (AF187148) drebrin E2 [Mus musculus]
+MAGVSFSGHRLELLAAYEEVIREESAADWALYTYEDGSDDLKLAASGEGGLQELSGHFENQKVMYGFCSV
+KDSQAALPTYVLINWVGEDVPDARKCACASHVAKVAEFFQGVDVIVNASSVEDIDAGAIGQRLSNGLARL
+SSPVLHRLRLREDENAEPVGTTYQKTDAAVEMKRINREQFWEQAKKEEELRKEEERKKALDARLRFEQER
+MEQERQEQEERERRYREREQQIEEHRRKQQSLEAEEAKRRLKEQSIFGDQRDEEEESQMKKSESEVEEAA
+AIIAQRPDNPREFFRQQERVASASGGSCDAPAPAPFNHRPGSHLDSHRRMAPTPIPTRSPSDSSTASTPI
+AEQIERALDEVTSSQPPPPPPPPPPTQEAQETTPSLDEELSKEAKVTAAPEVWAGCAAEPPQAQEPPLLQ
+SSPLEDSMCTESPEQAALAAPAEPAASVTSVADVHAADTIETTTATTDTTIANNVTPAAASLIDLWPGNG
+EEASTLQAEPRVPTPPSGAEASLAEVPLLNEAAQEPLPPVGEGCANLLNFDELPEPPATFCDPEEEVGET
+LAASQVLTMPSALEEVDQVLEQELEPEPHLLTNGETTQKEGTQASEGYFSQSQEEEFAQSEEPCAKVPPP
+VFYNKPPEIDITCWDADPVPEEEEGFEGGD
+>gi|6694235|gb|AAF25193.1|AF190151_1 (AF190151) testis-specific calpastatin, short form [Mus musculus]
+MGQFLSSTFWEGSPAAVWQEKLREGERKGAGETIPILQDHAKAKEERQEKCGEDEDTVPAEYRLKPAKDK
+DGKPLLPEPEETSKSLSESELIGELSADFDRSTYQDKPSTPAEKKSNDTSQTPPGETVPRASMCSIRSAP
+PKLASLKGVVPEDAVETLAGSLGTREADPEHEKTVEDKVKEKAKEEEHEKLGEKEETVPPDYRLEEVKDK
+DGKPLLPKESQEQLAPLSDDFLLDALSQDFSSPANISSLEFEDAKLSAAISEVVSQTPAPSTHAAAPLPG
+TEQKDKELDDALDELSDSLGQRPPDPDENKPLDDKVKEKIKPEHSEKLGERDDTIPPEYRHLLDNDGKDK
+PEKPPTKKTEKPDQDRDPIDALSEDLDSCPSTTETSKNTAKGKSKKTSSSKASKDGEKTKDSSKKTEEVS
+KPKAKEDARHS
+>gi|6694237|gb|AAF25194.1|AF190152_1 (AF190152) testis-specific calpastatin, long form [Mus musculus]
+MGQFLSSTFWEGSPAAVWQEKLREGERKGAGETIPILQDHVICSEEREHGSKHHEAKAKEERQEKCGEDE
+DTVPAEYRLKPAKDKDGKPLLPEPEETSKSLSESELIGELSADFDRSTYQDKPSTPAEKKSNDTSQTPPG
+ETVPRASMCSIRSAPPKLASLKGVVPEDAVETLAGSLGTREADPEHEKTVEDKVKEKAKEEEHEKLGEKE
+ETVPPDYRLEEVKDKDGKPLLPKESQEQLAPLSDDFLLDALSQDFSSPANISSLEFEDAKLSAAISEVVS
+QTPAPSTHAAAPLPGTEQKDKELDDALDELSDSLGQRPPDPDENKPLDDKVKEKIKPEHSEKLGERDDTI
+PPEYRHLLDNDGKDKPEKPPTKKTEKPDQDRDPIDALSEDLDSCPSTTETSKNTAKGKSKKTSSSKASKD
+GEKTKDSSKKTEEVSKPKAKEDARHS
+>gi|6694239|gb|AAF25195.1|AF190639_1 (AF190639) cAMP-specific phosphodiesterase PDE7B [Mus musculus]
+MSCLMVERCGEVLFESPEQSVKCVCMLGDVRLRGQTGVPAERRGSYPFIDFRLLNNTTHSGEIGTKKKVK
+RLLSFQRYFHASRLLRGIIPQAPLHLLDEDYLGQARHMLSKVGTWDFDIFLFDRLTNGNSLVTLLCHLFN
+SHGLIHHFKLDMVTLHRFLVMVQEDYHGHNPYHNAVHAADVTQAMHCYLKEPKLASFLTPLDIMLGLLAA
+AAHDVDHPGVNQPFLIKTNHHLANLYQNMSVLENHHWRSTIGMLRESRLLAHLPKEMTQDIEQQLGSLIL
+ATDINRQNEFLTRLKAHLHNKDLRLENVQDRHFMLQIALKCADICNPCRIWEMSKQWSERVCEEFYRQGD
+LEQKFELEISPLCNQQKDSIPSIQIGFMTYIVEPLFREWARFTGNSTLSENMLSHLAHNKAQWKSLLSNQ
+HRRRGSGQDLAGPAPETLEQTEGATP
+>gi|6694257|gb|AAF25196.1| (AF191558) hepatocyte nuclear factor-3 beta [Mus musculus]
+MLGAVKMEGHEPSDWSSYY
+>gi|6694274|gb|AAF25197.1|AF193553_1 (AF193553) ubiquitin-like protein activating enzyme [Drosophila melanogaster]
+MAAAINGVFPPTLQELVKKSKVLVVGAGGIGCEVLKNLVLSGFTDIEIIDLDTIDLSNLNRQFLFHREHV
+GKSKARVARESALSFNPDAKITAYHDSVTSTDYGVNFFKKFDLVLSALDNRAARNHVNRMCLNADVPLIE
+SGTAGYNGQVELIKRGLTQCYECTPKDKQRSFPGCTIRNTPSEPIHCIVWAKHLFNQLFGESLEDEDISP
+DAADPDAKEKDGGDGNGEPKGDGKEKGEESKEEKEAKEDTANGNIMRINTRQWAKDSNYDAGKLFNKFFN
+EDITYLLRMSNLWKTRKAPVPVQWDTLLPEGSSGDQKDVAKQHHKVWSIEECAQVFANSLKELSANFLKL
+EGDDTLAWDKDDQPAMDFVAACANVRSHIFDIERKSRFEIKSMAGNIIPAIATTNAITAGISVMRAFKVL
+EAKWEQCKAVYARLRPNARNHFLVPDASLPGPNPNCHVCASDPAITLKIDTKRMRIKELRDEVLVKTLNM
+LNPDVTVQSNGSILISSEEGETECNDGKLLSELNIVDGVILKCDDFFQNYELSIIISHFDAERDENLFEV
+VADASQLKPKDEDQKEAVKDKEDEPKSAKKRSTNGEGDSKDDGPSTSKRSRPNEVVEEDDDDCLVIEEDE
+DQADVVVVATDKLSVQSPPKSGSKRKPCEVIEDEDITEILESSDDEPAGPTKCKRSRLDDSNPVAVISID
+>gi|6694276|gb|AAF25198.1|AF193554_1 (AF193554) ubiquitin-like protein activating enzyme N subunit [Drosophila melanogaster]
+MVVDMDTSETAVELTEAENELYDRQIRLWGLESQKRLRTAKILIAGLCGLGAEITKNIILSGVNSVKLLD
+DKDVTEEDFCSQFLVPRESLNTNRAEASLTRARALNPMVDISADREPLKEKTSEFFGQFDVVVVNGATNE
+ELLRIDTICRDLGVKFIATDVWGTFGFYFASLQKHSYVEDVIKHKVVANSEKKKKYETVSIPTQRDVDYP
+GYSAWLDFDVTEPSYLRKLKRNGPGVLLLSVLQKFRTTHKRDPSYKTREADLELLRGIRDELLPNSILGN
+EALGLIFAQISPAVAVVGGVVAQEVIKVVTKLEAPHRNLFVFDPETCAGYVEAIGAK
+>gi|6694278|gb|AAF25199.1|AF193613_1 (AF193613) cell recognition molecule Caspr2 [Homo sapiens]
+MQAAPRAGCGAALLLWIVSSCLCRAWTAPSTSQKCDEPLVSGLPHVAFSSSSSISGSYSPGYAKINKRGG
+AGGWSPSDSDHYQWLQVDFGNRKQISAIATQGRYSSSDWVTQYRMLYSDTGRNWKPYHQDGNIWAFPGNI
+NSDGVVRHELQHPIIARYVRIVPLDWNGEGRIGLRIEVYGCSYWADVINFDGHVVLPYRFRNKKMKTLKD
+VIALNFKTSESEGVILHGEGQQGDYITLELKKAKLVLSLNLGSNQLGPIYGHTSVMTGSLLDDHHWHSVV
+IERQGRSINLTLDRSMQHFRTNGEFDYLDLDYEITFGGIPFSGKPSSSSRKNFKGCMESINYNGVNITDL
+ARRKKLEPSNVGNLSFSCVEPYTVPVFFNATSYLEVPGRLNQDLFSVSFQFRTWNPNGLLVFSHFADNLG
+NVEIDLTESKVGVHINITQTKMSQIDISSGSGLNDGQWHEVRFLAKENFAILTIDGDEASAVRTNSPLQV
+KTGEKYFFGGFLNQMNNSSHSVLQPSFQGCMQLIQVDDQLVNLYEVAQRKPGSFANVSIDMCAIIDRCVP
+NHCEHGGKCSQTWDSFKCTCDETGYSGATCHNSIYEPSCEAYKHLGQTSNYYWIDPDGSGPLGPLKVYCN
+MTEDKVWTIVSHDLQMQTPVVGYNPEKYSVTQLVYSASMDQISAITDSAEYCEQYVSYFCKMSRLLNTPD
+GSPYTWWVGKANEKHYYWGGSGPGIQKCACGIERNCTDPKYYCNCDADYKQWRKDAGFLSYKDHLPVSQV
+VVGDTDRQGSEAKLSVGPLRCQGDRNYWNAASFPNPSSYLHFSTFQGETSADISFYFKTLTPWGVFLENM
+GKEDFIKLELKSATEVSFSFDVGNGPVEIVVRSPTPLNDDQWHRVTAERNVKQASLQVDRLPQQIRKAPT
+EGHTRLELYSQLFVGGAGGQQGFLGCIRSLRMNGVTLDLEERAKVTSGFISGCSGHCTSYGTNCENGGKC
+LERYHGYSCDCSNTAYDGTFCNKDVGAFFEEGMWLRYNFQAPATNARDSSSRVDNAPDQQNSHPDLAQEE
+IRFSFSTTKAPCILLYISSFTTDFLAVLVKPTGSLQIRYNLGGTREPYNIDVDHRNMANGQPHSVNITRH
+EKTIFLKLDHYPSVSYHLPSSSDTLFNSPKSLFLGKVIETGKIDQEIHKYNTPGFTGCLSRVQFNQIAPL
+KAALRQTNASAHVHIQGELVESNCGASPLTLSPMSSATDPWHLDHLDSASADFPYNPGQGQAIRNGVNRN
+SAIIGGVIAVVIFTILCTLVFLIRYMFRHKGTYHTNEAKGAESAESADAAIMNNDPNFTETIDESKKEWL
+I
+>gi|6694282|gb|AAF25200.1|AF196838_1 (AF196838) coat protein [Papaya ringspot virus]
+NTHVFHQSKNEAVDAGLNEKLKEKEKQKEKERQREKEKVDASDGKNVSTSTKIGERDKDVNVGTSGTFTV
+PRIKSFTDKMTLPRIKGKAVLNLNHLLQYNPQQIDISNTRATQSQFEKWYEGVRSDYGLNDNEMQVMLNG
+LMVWCIENGTSPDISGVWVMMDEETQVDYPIKPLIEHANPSFRQIMAHFSNAAEAYIAKRNATERYMPRY
+GIKRNLTDISLARYAFDFYEVNSKTPDRAREAHMQMKAAALRNTSRRMFGIDGSVSNKEENTERHTVEDV
+NRDMHSLLGMRN
+>gi|6694284|gb|AAF25201.1|AF196839_1 (AF196839) coat protein [Papaya ringspot virus]
+NTHVFHQSKNEAVDAGLNEKLKEKEKQKEKEKEKQKEKDDASDGNDVSTSTKTGERDRDVNVGTSGTFTV
+PRIKSFTDKMILPRIKGKTVLNLNHLLQYNPQQIDISNTRATQSQFEKWYEGVRSDYGLNDNEMQVTLNG
+LMVWCIENGTSPDISGVWVMMDGETQVDYPIKPLIEHATPSFRQIMAHFSNAAEAYIAKRNATERYMPRY
+GIKRNLTDISLARYAFDFYEVNSKTPDRAREAHMQMKAAALRNASRRMFGMDGSVSNKEENTERHTVEDV
+NRDMHSLLGMRN
+>gi|6694286|gb|AAF25202.1| (AF197127) unknown [Mus musculus]
+MKVDVGPDPSLVYRPDVDPEMAKSKDSFRNYTSGPLLDRVFTTYKLMHTHQTVDFVSRKRIQYGGFSYKK
+MTIMEAVGMLDDLVDESDPDVDFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKIMALWGEPQWAVV
+GDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGMYQPHCGLENVLMSWGHDEYLYQMMKFNKFSLP
+SEAFYMIRFHSFYPWHTGGDYRQLCSQQDLDMLPWVQEFNKFDLYTKCPDLPDVESLRPYYQGLIDKYCP
+GTLSW
+>gi|6694288|gb|AAF25203.1| (AF197128) unknown [Rattus norvegicus]
+MKVDLGPDPSLVYRPDVDPEMAKSKGSFRNYTSGPLLDRVFTTYKLMHTHQTVDFVMRKRIQFGSFSYKK
+MTVMEAVDMLDDLVDESDPDVDFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKILALWGEPQWAVV
+GDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGMYQPHCGLENVLMSWGHDEYLYQMMKFNKFSLP
+SEAFYMVRFHSFYPWHTGGDYRQLCSQQDLDMLPWVQEFNKFDLYTKCPDLPEVKSLRPYYQGLIDKYCP
+GTLSW
+>gi|6694290|gb|AAF25204.1| (AF197129) unknown [Homo sapiens]
+MKVDVGPDPSLVYRPDVDPEVAKDKASFRNYTSGPLLDRVFTTYKLMHTHQTVDFVRSKHAQFGGFSYKK
+MTVMEAVDLLDGLVDESDPDVDFPNSFHAFQTAEGIRKAHPDKDWFHLVGLLHDLGKVLALFGEPQWAVV
+GDTFPVGCRPQASVVFCDSTFQDNPDLQDPRYSTELGMYQPHCGLDRVLMSWGHDEYMYQVMKFNKFSLP
+PEAFYMIRFHSFYPWHTGRDYQQLCSQQDLAMLPWVREFNKFDLYTKCPDLPDVDKLRPYYQGLIDKYCP
+GTLSW
+>gi|6694369|gb|AAF25205.1|AF199509_1 (AF199509) NADPH-dependent FMN and FAD containing oxidoreductase [Homo sapiens]
+MPSPQLLVLFGSQTGTAQDVSERLGREARRRRLGCRVQALDSYPVVNLINEPLVIFVCATTGQGDPPDNM
diff --git a/network/wwwblast/db/test_aa_db.phr b/network/wwwblast/db/test_aa_db.phr
new file mode 100644
index 00000000..d48d6437
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db.phr
@@ -0,0 +1 @@
+gi|6693791|gb|AAF24984.1|AF082179_1 (AF082179) HepA-related protein HARP [Homo sapiens]gi|6693793|gb|AAF24985.1|AF088884_1 (AF088884) HepA-related protein Harp [Mus musculus]gi|6693798|gb|AAF24986.1|AF116242_1 (AF116242) K-Cl cotransporter KCC3 [Homo sapiens]gi|6693800|gb|AAF24987.1|AF121349_1 (AF121349) HOAR-like protein [Neodiprion sertifer nucleopolyhedrovirus]gi|6693801|gb|AAF24988.1|AF121349_2 (AF121349) ORF22 [Neodiprion sertifer nucleopolyhedrovirus]gi|6693802|gb|AAF24989.1|AF121349_3 (AF121349) late expression factor 2 [Neodiprion sertifer nucleopolyhedrovirus]gi|6693803|gb|AAF24990.1|AF121349_4 (AF121349) late expression factor 5 [Neodiprion sertifer nucleopolyhedrovirus]gi|6693805|gb|AAF24991.1| (AF125506) astacin family metalloendopeptidase FARM-1 [Hydra vulgaris]gi|6693816|gb|AAF24994.1|AF129447_1 (AF129447) RpoB [Klebsiella ornithinolytica]gi|6693818|gb|AAF24995.1|AF129448_1 (AF129448) RpoB [Klebsiella terrigena]gi|6693824|gb|AAF24998.1|AF134213_1 (AF134213) ubiquitin-specific protease [Homo sapiens]gi|6693827|gb|AAF24999.1| (AF141320) endo-inulinase [Pseudomonas mucidolens]gi|6693829|gb|AAF25000.1|AF153207_1 (AF153207) proline dehydrogenase [Pseudomonas putida]gi|6693830|gb|AAF25001.1|AF153207_2 (AF153207) proline permease [Pseudomonas putida]gi|6693832|gb|AAF25002.1|AF156878_1 (AF156878) opioid growth factor receptor [Rattus norvegicus]gi|6693834|gb|AAF25003.1|AF156981_1 (AF156981) SNIP-a [Rattus norvegicus]gi|6693836|gb|AAF25004.1|AF156982_1 (AF156982) SNIP-b [Rattus norvegicus]gi|6693838|gb|AAF25005.1|AF158184_1 (AF158184) 14-kDa diagnostic antigen [Taenia solium]gi|6693854|gb|AAF25008.1|AF176679_1 (AF176679) salmonase [Gloydius halys brevicaudus]gi|6693856|gb|AAF25009.1|AF177945_1 (AF177945) superoxide dismutase [Nostoc commune]gi|6693870|gb|AAF25010.1|AF179404_1 (AF179404) UDP-glucuronosyltransferase UGT2B15 [Homo sapiens]gi|6693872|gb|AAF25011.1| (AF181288) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693874|gb|AAF25012.1| (AF181289) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693876|gb|AAF25013.1| (AF181290) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693878|gb|AAF25014.1| (AF181291) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693880|gb|AAF25015.1| (AF181292) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693882|gb|AAF25016.1| (AF181293) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693884|gb|AAF25017.1| (AF181294) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693886|gb|AAF25018.1| (AF181295) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693888|gb|AAF25019.1| (AF181296) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693890|gb|AAF25020.1| (AF181297) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693892|gb|AAF25021.1| (AF181298) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693894|gb|AAF25022.1| (AF181299) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693896|gb|AAF25023.1| (AF181300) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693898|gb|AAF25024.1| (AF181301) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693900|gb|AAF25025.1| (AF181302) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693902|gb|AAF25026.1| (AF181303) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693904|gb|AAF25027.1| (AF181304) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693906|gb|AAF25028.1| (AF181305) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693908|gb|AAF25029.1| (AF181306) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693910|gb|AAF25030.1| (AF181307) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693912|gb|AAF25031.1| (AF181308) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693914|gb|AAF25032.1| (AF181309) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693916|gb|AAF25033.1| (AF181310) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693918|gb|AAF25034.1| (AF181311) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693920|gb|AAF25035.1| (AF181312) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693922|gb|AAF25036.1| (AF181313) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693924|gb|AAF25037.1| (AF181314) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693926|gb|AAF25038.1| (AF181315) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693928|gb|AAF25039.1| (AF181316) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693930|gb|AAF25040.1| (AF181317) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693932|gb|AAF25041.1| (AF181318) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693934|gb|AAF25042.1| (AF181319) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693936|gb|AAF25043.1| (AF181320) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693938|gb|AAF25044.1| (AF181321) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693940|gb|AAF25045.1| (AF181322) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693942|gb|AAF25046.1| (AF181323) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693944|gb|AAF25047.1| (AF181324) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693946|gb|AAF25048.1| (AF181325) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693948|gb|AAF25049.1| (AF181326) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693950|gb|AAF25050.1| (AF181327) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693952|gb|AAF25051.1| (AF181328) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693954|gb|AAF25052.1| (AF181329) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693956|gb|AAF25053.1| (AF181330) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693958|gb|AAF25054.1| (AF181331) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693960|gb|AAF25055.1| (AF181332) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693962|gb|AAF25056.1| (AF181333) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693964|gb|AAF25057.1| (AF181334) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693966|gb|AAF25058.1| (AF181335) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693968|gb|AAF25059.1| (AF181336) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693970|gb|AAF25060.1| (AF181337) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693972|gb|AAF25061.1| (AF181338) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693974|gb|AAF25062.1| (AF181339) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693976|gb|AAF25063.1| (AF181340) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693978|gb|AAF25064.1| (AF181341) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693980|gb|AAF25065.1| (AF181342) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693982|gb|AAF25066.1| (AF181343) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693984|gb|AAF25067.1| (AF181344) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693986|gb|AAF25068.1| (AF181345) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693988|gb|AAF25069.1| (AF181346) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693990|gb|AAF25070.1| (AF181347) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693992|gb|AAF25071.1| (AF181348) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693994|gb|AAF25072.1| (AF181349) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693996|gb|AAF25073.1| (AF181350) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6693998|gb|AAF25074.1| (AF181351) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694000|gb|AAF25075.1| (AF181352) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694002|gb|AAF25076.1| (AF181353) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694004|gb|AAF25077.1| (AF181354) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694006|gb|AAF25078.1| (AF181355) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694008|gb|AAF25079.1| (AF181356) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694010|gb|AAF25080.1| (AF181357) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694012|gb|AAF25081.1| (AF181358) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694014|gb|AAF25082.1| (AF181359) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694016|gb|AAF25083.1| (AF181360) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694018|gb|AAF25084.1| (AF181361) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694020|gb|AAF25085.1| (AF181362) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694022|gb|AAF25086.1| (AF181363) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694024|gb|AAF25087.1| (AF181364) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694026|gb|AAF25088.1| (AF181365) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694028|gb|AAF25089.1| (AF181366) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694030|gb|AAF25090.1| (AF181367) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694032|gb|AAF25091.1| (AF181368) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694034|gb|AAF25092.1| (AF181369) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694036|gb|AAF25093.1| (AF181370) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694038|gb|AAF25094.1| (AF181371) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694040|gb|AAF25095.1| (AF181372) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694042|gb|AAF25096.1| (AF181373) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694044|gb|AAF25097.1| (AF181374) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694046|gb|AAF25098.1| (AF181375) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694048|gb|AAF25099.1| (AF181376) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694050|gb|AAF25100.1| (AF181377) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694052|gb|AAF25101.1| (AF181378) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694054|gb|AAF25102.1| (AF181379) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694056|gb|AAF25103.1| (AF181380) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694058|gb|AAF25104.1| (AF181381) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694060|gb|AAF25105.1| (AF181382) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694062|gb|AAF25106.1| (AF181383) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694064|gb|AAF25107.1| (AF181384) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694066|gb|AAF25108.1| (AF181385) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694068|gb|AAF25109.1| (AF181386) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694070|gb|AAF25110.1| (AF181387) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694072|gb|AAF25111.1| (AF181388) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694074|gb|AAF25112.1| (AF181389) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694076|gb|AAF25113.1| (AF181390) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694078|gb|AAF25114.1| (AF181391) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694080|gb|AAF25115.1| (AF181392) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694082|gb|AAF25116.1| (AF181393) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694084|gb|AAF25117.1| (AF181394) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694086|gb|AAF25118.1| (AF181395) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694088|gb|AAF25119.1| (AF181396) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694090|gb|AAF25120.1| (AF181397) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694092|gb|AAF25121.1| (AF181398) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694094|gb|AAF25122.1| (AF181399) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694096|gb|AAF25123.1| (AF181400) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694098|gb|AAF25124.1| (AF181401) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694100|gb|AAF25125.1| (AF181402) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694102|gb|AAF25126.1| (AF181403) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694104|gb|AAF25127.1| (AF181404) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694106|gb|AAF25128.1| (AF181405) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694108|gb|AAF25129.1| (AF181406) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694110|gb|AAF25130.1| (AF181407) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694112|gb|AAF25131.1| (AF181408) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694114|gb|AAF25132.1| (AF181409) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694116|gb|AAF25133.1| (AF181410) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694118|gb|AAF25134.1| (AF181411) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694120|gb|AAF25135.1| (AF181412) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694122|gb|AAF25136.1| (AF181413) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694124|gb|AAF25137.1| (AF181414) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694126|gb|AAF25138.1| (AF181415) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694128|gb|AAF25139.1| (AF181416) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694130|gb|AAF25140.1| (AF181417) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694132|gb|AAF25141.1| (AF181418) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694134|gb|AAF25142.1| (AF181419) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694136|gb|AAF25143.1| (AF181420) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694138|gb|AAF25144.1| (AF181421) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694140|gb|AAF25145.1| (AF181422) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694142|gb|AAF25146.1| (AF181423) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694144|gb|AAF25147.1| (AF181424) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694146|gb|AAF25148.1| (AF181425) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694148|gb|AAF25149.1| (AF181426) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694150|gb|AAF25150.1| (AF181427) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694152|gb|AAF25151.1| (AF181428) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694154|gb|AAF25152.1| (AF181429) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694156|gb|AAF25153.1| (AF181430) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694158|gb|AAF25154.1| (AF181431) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694160|gb|AAF25155.1| (AF181432) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694162|gb|AAF25156.1| (AF181433) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694164|gb|AAF25157.1| (AF181434) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694166|gb|AAF25158.1| (AF181435) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694168|gb|AAF25159.1| (AF181436) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694170|gb|AAF25160.1| (AF181437) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694172|gb|AAF25161.1| (AF181438) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694174|gb|AAF25162.1| (AF181439) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694176|gb|AAF25163.1| (AF181440) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694178|gb|AAF25164.1| (AF181441) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694180|gb|AAF25165.1| (AF181442) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694182|gb|AAF25166.1| (AF181443) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694184|gb|AAF25167.1| (AF181444) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694186|gb|AAF25168.1| (AF181445) envelope glycoprotein [Human immunodeficiency virus type 1]gi|6694188|gb|AAF25169.1|AF182341_1 (AF182341) NADH dehydrogenase [Buergersiochloa bambusoides]gi|6694190|gb|AAF25170.1|AF182342_1 (AF182342) NADH dehydrogenase [Shibataea kumasaca]gi|6694192|gb|AAF25171.1|AF182343_1 (AF182343) NADH dehydrogenase [Sucrea maculata]gi|6694194|gb|AAF25172.1|AF182344_1 (AF182344) NADH dehydrogenase [Sasa variegata]gi|6694196|gb|AAF25173.1|AF182345_1 (AF182345) NADH dehydrogenase [Puelia olyriformis]gi|6694198|gb|AAF25174.1|AF182346_1 (AF182346) NADH dehydrogenase [Yushania exilis]gi|6694200|gb|AAF25175.1|AF182347_1 (AF182347) NADH dehydrogenase [Alvimia gracilis]gi|6694202|gb|AAF25176.1|AF182348_1 (AF182348) NADH dehydrogenase [Melocanna baccifera]gi|6694204|gb|AAF25177.1|AF182349_1 (AF182349) NADH dehydrogenase [Rhipidocladum pittieri]gi|6694206|gb|AAF25178.1|AF182350_1 (AF182350) NADH dehydrogenase [Otatea acuminata]gi|6694208|gb|AAF25179.1|AF182351_1 (AF182351) NADH dehydrogenase [Hickelia madagascariensis]gi|6694210|gb|AAF25180.1|AF182352_1 (AF182352) NADH dehydrogenase [Nastus elatus]gi|6694212|gb|AAF25181.1|AF182353_1 (AF182353) NADH dehydrogenase [Eremitis sp. Clark and Zhang 1343]gi|6694214|gb|AAF25182.1|AF182354_1 (AF182354) NADH dehydrogenase [Pariana radiciflora]gi|6694216|gb|AAF25183.1|AF182355_1 (AF182355) NADH dehydrogenase [Neurolepis aperta]gi|6694218|gb|AAF25184.1|AF182402_1 (AF182402) metalloregulator RmtA [Streptococcus gordonii]gi|6694219|gb|AAF25185.1|AF182402_2 (AF182402) unknown [Streptococcus gordonii]gi|6694221|gb|AAF25186.1|AF182949_1 (AF182949) voltage-gated sodium channel subunit beta1-A [Rattus norvegicus]gi|6694223|gb|AAF25187.1|AF184244_1 (AF184244) ribonucleoprotein [Danio rerio]gi|6694225|gb|AAF25188.1|AF184245_1 (AF184245) ribonucleoprotein [Danio rerio]gi|6694227|gb|AAF25189.1|AF187147_1 (AF187147) drebrin A [Mus musculus]gi|6694229|gb|AAF25190.1|AF187148_1 (AF187148) drebrin E2 [Mus musculus]gi|6694235|gb|AAF25193.1|AF190151_1 (AF190151) testis-specific calpastatin, short form [Mus musculus]gi|6694237|gb|AAF25194.1|AF190152_1 (AF190152) testis-specific calpastatin, long form [Mus musculus]gi|6694239|gb|AAF25195.1|AF190639_1 (AF190639) cAMP-specific phosphodiesterase PDE7B [Mus musculus]gi|6694257|gb|AAF25196.1| (AF191558) hepatocyte nuclear factor-3 beta [Mus musculus]gi|6694274|gb|AAF25197.1|AF193553_1 (AF193553) ubiquitin-like protein activating enzyme [Drosophila melanogaster]gi|6694276|gb|AAF25198.1|AF193554_1 (AF193554) ubiquitin-like protein activating enzyme N subunit [Drosophila melanogaster]gi|6694278|gb|AAF25199.1|AF193613_1 (AF193613) cell recognition molecule Caspr2 [Homo sapiens]gi|6694282|gb|AAF25200.1|AF196838_1 (AF196838) coat protein [Papaya ringspot virus]gi|6694284|gb|AAF25201.1|AF196839_1 (AF196839) coat protein [Papaya ringspot virus]gi|6694286|gb|AAF25202.1| (AF197127) unknown [Mus musculus]gi|6694288|gb|AAF25203.1| (AF197128) unknown [Rattus norvegicus]gi|6694290|gb|AAF25204.1| (AF197129) unknown [Homo sapiens]gi|6694369|gb|AAF25205.1|AF199509_1 (AF199509) NADPH-dependent FMN and FAD containing oxidoreductase [Homo sapiens]
\ No newline at end of file
diff --git a/network/wwwblast/db/test_aa_db.pin b/network/wwwblast/db/test_aa_db.pin
new file mode 100644
index 00000000..ff74fdb4
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db.pin
diff --git a/network/wwwblast/db/test_aa_db.pnd b/network/wwwblast/db/test_aa_db.pnd
new file mode 100644
index 00000000..3a92c1ac
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db.pnd
diff --git a/network/wwwblast/db/test_aa_db.pni b/network/wwwblast/db/test_aa_db.pni
new file mode 100644
index 00000000..58ddb18d
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db.pni
diff --git a/network/wwwblast/db/test_aa_db.psd b/network/wwwblast/db/test_aa_db.psd
new file mode 100644
index 00000000..c676afc6
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db.psd
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+gi|669391844
+gi|669392045
+gi|669392246
+gi|669392447
+gi|669392648
+gi|669392849
+gi|669393050
+gi|669393251
+gi|669393452
+gi|669393653
+gi|669393854
+gi|669394055
+gi|669394256
+gi|669394457
+gi|669394658
+gi|669394859
+gi|669395060
+gi|669395261
+gi|669395462
+gi|669395663
+gi|669395864
+gi|669396065
+gi|669396266
+gi|669396467
+gi|669396668
+gi|669396869
+gi|669397070
+gi|669397271
+gi|669397472
+gi|669397673
+gi|669397874
+gi|669398075
+gi|669398276
+gi|669398477
+gi|669398678
+gi|669398879
+gi|669399080
+gi|669399281
+gi|669399482
+gi|669399683
+gi|669399884
+gi|669400085
+gi|669400286
+gi|669400487
+gi|669400688
+gi|669400889
+gi|669401090
+gi|669401291
+gi|669401492
+gi|669401693
+gi|669401894
+gi|669402095
+gi|669402296
+gi|669402497
+gi|669402698
+gi|669402899
+gi|6694030100
+gi|6694032101
+gi|6694034102
+gi|6694036103
+gi|6694038104
+gi|6694040105
+gi|6694042106
+gi|6694044107
+gi|6694046108
+gi|6694048109
+gi|6694050110
+gi|6694052111
+gi|6694054112
+gi|6694056113
+gi|6694058114
+gi|6694060115
+gi|6694062116
+gi|6694064117
+gi|6694066118
+gi|6694068119
+gi|6694070120
+gi|6694072121
+gi|6694074122
+gi|6694076123
+gi|6694078124
+gi|6694080125
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+gi|6694086128
+gi|6694088129
+gi|6694090130
+gi|6694092131
+gi|6694094132
+gi|6694096133
+gi|6694098134
+gi|6694100135
+gi|6694102136
+gi|6694104137
+gi|6694106138
+gi|6694108139
+gi|6694110140
+gi|6694112141
+gi|6694114142
+gi|6694116143
+gi|6694118144
+gi|6694120145
+gi|6694122146
+gi|6694124147
+gi|6694126148
+gi|6694128149
+gi|6694130150
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+gi|6694134152
+gi|6694136153
+gi|6694138154
+gi|6694140155
+gi|6694142156
+gi|6694144157
+gi|6694146158
+gi|6694148159
+gi|6694150160
+gi|6694152161
+gi|6694154162
+gi|6694156163
+gi|6694158164
+gi|6694160165
+gi|6694162166
+gi|6694164167
+gi|6694166168
+gi|6694168169
+gi|6694170170
+gi|6694172171
+gi|6694174172
+gi|6694176173
+gi|6694178174
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+gi|6694184177
+gi|6694186178
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+gi|6694200185
+gi|6694202186
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+gi|6694206188
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+gi|6694212191
+gi|6694214192
+gi|6694216193
+gi|6694218194
+gi|6694219195
+gi|6694221196
+gi|6694223197
+gi|6694225198
+gi|6694227199
+gi|6694229200
+gi|6694235201
+gi|6694237202
+gi|6694239203
+gi|6694257204
+gi|6694274205
+gi|6694276206
+gi|6694278207
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+gi|6694290212
+gi|6694369213
diff --git a/network/wwwblast/db/test_aa_db.psi b/network/wwwblast/db/test_aa_db.psi
new file mode 100644
index 00000000..df390670
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db.psi
diff --git a/network/wwwblast/db/test_aa_db.psq b/network/wwwblast/db/test_aa_db.psq
new file mode 100644
index 00000000..0c2fad3a
--- /dev/null
+++ b/network/wwwblast/db/test_aa_db.psq
diff --git a/network/wwwblast/db/test_na_db b/network/wwwblast/db/test_na_db
new file mode 100644
index 00000000..cb4c11fe
--- /dev/null
+++ b/network/wwwblast/db/test_na_db
@@ -0,0 +1,1000 @@
+>gi|1786181|gb|AE000111|ECAE000111 Escherichia coli , thrL, thrA, thrB, thrC, yaaA, yaaJ, talB, mog, yaaH genes from bases 1 to 10596 (section 1 of 400) of the complete genome
+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC
+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA
+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC
+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG
+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA
+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC
+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG
+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT
+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT
+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC
+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT
+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT
+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG
+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC
+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT
+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG
+CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC
+CGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC
+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGG
+CGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGA
+ATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTC
+TACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGG
+TAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATAT
+CAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG
+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG
+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA
+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG
+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA
+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC
+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC
+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG
+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT
+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG
+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA
+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT
+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC
+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG
+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA
+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC
+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC
+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG
+TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA
+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG
+CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT
+CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC
+GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC
+GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC
+AAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC
+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTC
+ATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT
+ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAG
+CGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCC
+GACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGG
+GCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC
+GCAAGCCGTAACCCAGGGGTTGGGCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGC
+CTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTA
+TTGGTGATGAAATCCCACAGGAAATCCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGT
+CGCCAATGTTGAAAGCGATGTCGGTTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTC
+GGCGGTCGCTTTATGGCACAAATGCTGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGA
+CCTCCGGTGATACCGGAGCGGCAGTGGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCT
+CTATCCACGAGGCAAAATCAGTCCACTGCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACT
+GTTGCCATCGACGGCGATTTCGATGCCTGTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAAGAACTGA
+AAGTGGCGCTAGGGTTAAACTCGGCTAACTCGATTAACATCAGCCGTTTGCTGGCGCAGATTTGCTACTA
+CTTTGAAGCTGTTGCGCAGCTGCCGCAGGAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAAC
+TTCGGCGATTTGACGGCGGGTCTGCTGGCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGA
+CCAACGTGAACGATACCGTGCCACGTTTCCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGAC
+GTTATCCAACGCGATGGACGTGAGTCAGCCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAA
+ATCTGGCAACTGAAAGAGCTGGGTTATGCAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGT
+TAAAAGAACTGGGCTACACTTCGGAGCCGCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAA
+TCCAGGCGAATATGGCTTGTTCCTCGGCACCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATT
+CTCGGTGAAACGTTGGATCTGCCAAAAGAGCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATC
+TGCCCGCCGATTTTGCTGCGTTGCGTAAATTGATGATGAATCATCAGTAAAATCTATTCATTATCTCAAT
+CAGGCCGGGTTTGCTTTTATGCAGCCCGGCTTTTTTATGAAGAAATTATGGAGAAAAATGACAGGGAAAA
+AGGAGAAATTCTCAATAAATGCGGTAACTTAGAGATTAGGATTGCGGAGAATAACAACCGCCGTTCTCAT
+CGAGTAATCTCCGGATATCGACCCATAACGGGCAATGATAAAAGGAGTAACCTGTGAAAAAGATGCAATC
+TATCGTACTCGCACTTTCCCTGGTTCTGGTCGCTCCCATGGCAGCACAGGCTGCGGAAATTACGTTAGTC
+CCGTCAGTAAAATTACAGATAGGCGATCGTGATAATCGTGGCTATTACTGGGATGGAGGTCACTGGCGCG
+ACCACGGCTGGTGGAAACAACATTATGAATGGCGAGGCAATCGCTGGCACCTACACGGACCGCCGCCACC
+GCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGGTCATGGTCCAGGCAAACATCACCGCTAA
+ATGACAAATGCCGGGTAACAATCCGGCATTCAGCGCCTGATGCGACGCTGGCGCGTCTTATCAGGCCTAC
+GTTAATTCTGCAATATATTGAATCTGCATGCTTTTGTAGGCAGGATAAGGCGTTCACGCCGCATCCGGCA
+TTGACTGCAAACTTAACGCTGCTCGTAGCGTTTAAACACCAGTTCGCCATTGCTGGAGGAATCTTCATCA
+AAGAAGTAACCTTCGCTATTAAAACCAGTCAGTTGCTCTGGTTTGGTCAGCCGATTTTCAATAATGAAAC
+GACTCATCAGACCGCGTGCTTTCTTAGCGTAGAAGCTGATGATCTTAAATTTGCCGTTCTTCTCATCGAG
+GAACACCGGCTTGATAATCTCGGCATTCAATTTCTTCGGCTTCACCGATTTAAAATACTCATCTGACGCC
+AGATTAATCACCACATTATCGCCTTGTGCTGCGAGCGCCTCGTTCAGCTTGTTGGTGATGATATCTCCCC
+AGAATTGATACAGATCTTTCCCTCGGGCATTCTCAAGACGGATCCCCATTTCCAGACGATAAGGCTGCAT
+TAAATCGAGCGGGCGGAGTACGCCATACAAGCCGGAAAGCATTCGCAAATGCTGTTGGGCAAAATCGAAA
+TCGTCTTCGCTGAAGGTTTCGGCCTGCAAGCCGGTGTAGACATCACCTTTAAACGCCAGAATCGCCTGGC
+GGGCATTCGCCGGCGTGAAATCTGGCTGCCAGTCATGAAAGCGAGCGGCGTTGATACCCGCCAGTTTGTC
+GCTGATGCGCATCAGCGTGCTAATCTGCGGAGGCGTCAGTTTCCGCGCCTCATGGATCAACTGCTGGGAA
+TTGTCTAACAGCTCCGGCAGCGTATAGCGCGTGGTGGTCAACGGGCTTTGGTAATCAAGCGTTTTCGCAG
+GTGAAATAAGAATCAGCATATCCAGTCCTTGCAGGAAATTTATGCCGACTTTAGCAAAAAATGAGAATGA
+GTTGATCGATAGTTGTGATTACTCCTGCGAAACATCATCCCACGCGTCCGGAGAAAGCTGGCGACCGATA
+TCCGGATAACGCAATGGATCAAACACCGGGCGCACGCCGAGTTTACGCTGGCGTAGATAATCACTGGCAA
+TGGTATGAACCACAGGCGAGAGCAGTAAAATGGCGGTCAAATTGGTAATAGCCATGCAGGCCATTATGAT
+ATCTGCCAGTTGCCACATCAGCGGAAGGCTTAGCAAGGTGCCGCCGATGACCGTTGCGAAGGTGCAGATC
+CGCAAACACCAGATCGCTTTAGGGTTGTTCAGGCGTAAAAAGAAGAGATTGTTTTCGGCATAAATGTAGT
+TGGCAACGATGGAGCTGAAGGCAAACAGAATAACCACAAGGGTAACAAACTCAGCACCCCAGGAACCCAT
+TAGCACCCGCATCGCCTTCTGGATAAGCTGAATACCTTCCAGCGGCATGTAGGTTGTGCCGTTACCCGCC
+AGTAATATCAGCATGGCGCTTGCCGTACAGATGACCAGGGTGTCGATAAAAATGCCAATCATCTGGACAA
+TCCCTTGCGCTGCCGGATGCGGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGAACCCATTCC
+CGCCTCATTGGAAAACATACTGCGCTGAAAACCGTTAGTAATCGCCTGGCTTAAGGTATATCCCGCCGCG
+CCGCCTGCCGCTTCCTGCCAGCCAAAAGCACTCTCAAAAATAGACCAAATGACGTGGGGAAGTTGCCCGA
+TATTCATTACGCAAATTACCAGGCTGGTCAGTACCCAGATTATCGCCATCAACGGGACAAAGCCCTGCAT
+GAGCCGGGCGACGCCATGAAGACCGCGAGTGATTGCCAGCAGAGTAAAGACAGCGAGAATAATGCCTGTC
+ACCAGCGGGGGAAAATCAAAAGAAAAACTCAGGGCGCGGGCAACGGCGTTCGCTTGAACTCCGCTGAAAA
+TTATGCCATAGGCGATGAGCAAAAAGACGGCGAACAGAACGCCCATCCAGCGCATCCCCAGCCCGCGCGC
+CATATACCATGCCGGTCCGCCACGAAACTGCCCATTGACGTCACGTTCTTTATAAAGTTGTGCCAGAGAA
+CATTCGGCAAACGAGGTCGCCATGCCGATAAACGCGGCAACCCACATCCAAAAGACGGCTCCAGGTCCAC
+CGGCGGTAATAGCCAGCGCAACGCCGGCCAGGTTGCCGCTACCCACGCGCGCCGCAAGACTGGTACACAA
+TGACTGAAATGAGGTTAAACCGCCTGGCTGTGGATGAATGCTATTTTTAAGACTTTTGCCAAACTGGCGG
+ATGTAGCGAAACTGCACAAATCCGGTGCGAAAAGTGAACCAACAACCTGCGCCGAAGAGCAGGTAAATCA
+TTACCGATCCCCAAAGGACGCTGTTAATGAAGGAGAAAAAATCTGGCATGCATATCCCTCTTATTGCCGG
+TCGCGATGACTTTCCTGTGTAAACGTTACCAATTGTTTAAGAAGTATATACGCTACGAGGTACTTGATAA
+CTTCTGCGTAGCATACATGAGGTTTTGTATAAAAATGGCGGGCGATATCAACGCAGTGTCAGAAATCCGA
+AACAGTCTCGCCTGGCGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGCGTCGTGATATCATCAGGGC
+AGACCGGTTACATCCCCCTAACAAGCTGTTTAAAGAGAAATACTATCATGACGGACAAATTGACCTCCCT
+TCGTCAGTACACCACCGTAGTGGCCGACACTGGGGACATCGCGGCAATGAAGCTGTATCAACCGCAGGAT
+GCCACAACCAACCCTTCTCTCATTCTTAACGCAGCGCAGATTCCGGAATACCGTAAGTTGATTGATGATG
+CTGTCGCCTGGGCGAAACAGCAGAGCAACGATCGCGCGCAGCAGATCGTGGACGCGACCGACAAACTGGC
+AGTAAATATTGGTCTGGAAATCCTGAAACTGGTTCCGGGCCGTATCTCAACTGAAGTTGATGCGCGTCTT
+TCCTATGACACCGAAGCGTCAATTGCGAAAGCAAAACGCCTGATCAAACTCTACAACGATGCTGGTATTA
+GCAACGATCGTATTCTGATCAAACTGGCTTCTACCTGGCAGGGTATCCGTGCTGCAGAACAGCTGGAAAA
+AGAAGGCATCAACTGTAACCTGACCCTGCTGTTCTCCTTCGCTCAGGCTCGTGCTTGTGCGGAAGCGGGC
+GTGTTCCTGATCTCGCCGTTTGTTGGCCGTATTCTTGACTGGTACAAAGCGAATACCGATAAGAAAGAGT
+ACGCTCCGGCAGAAGATCCGGGCGTGGTTTCTGTATCTGAAATCTACCAGTACTACAAAGAGCACGGTTA
+TGAAACCGTGGTTATGGGCGCAAGCTTCCGTAACATCGGCGAAATTCTGGAACTGGCAGGCTGCGACCGT
+CTGACCATCGCACCGGCACTGCTGAAAGAGCTGGCGGAGAGCGAAGGGGCTATCGAACGTAAACTGTCTT
+ACACCGGCGAAGTGAAAGCGCGTCCGGCGCGTATCACTGAGTCCGAGTTCCTGTGGCAGCACAACCAGGA
+TCCAATGGCAGTAGATAAACTGGCGGAAGGTATCCGTAAGTTTGCTATTGACCAGGAAAAACTGGAAAAA
+ATGATCGGCGATCTGCTGTAATCATTCTTAGCGTGACCGGGAAGTCGGTCACGCTACCTCTTCTGAAGCC
+TGTCTGTCACTCCCTTCGCAGTGTATCATTCTGTTTAACGAGACTGTTTAAACGGAAAAATCTTGATGAA
+TACTTTACGTATTGGCTTAGTTTCCATCTCTGATCGCGCATCCAGCGGCGTTTATCAGGATAAAGGCATC
+CCTGCGCTGGAAGAATGGCTGACATCGGCGCTAACCACGCCGTTTGAACTGGAAACCCGCTTAATCCCCG
+ATGAGCAGGCGATCATCGAGCAAACGTTGTGTGAGCTGGTGGATGAAATGAGTTGCCATCTGGTGCTCAC
+CACGGGCGGAACTGGCCCGGCGCGTCGTGACGTAACGCCCGATGCGACGCTGGCAGTAGCGGACCGCGAG
+ATGCCTGGCTTTGGTGAACAGATGCGCCAGATCAGCCTGCATTTTGTACCAACTGCGATCCTTTCGCGTC
+AGGTGGGCGTGATTCGCAAACAGGCGCTGATCCTTAACTTACCCGGTCAGCCGAAGTCTATTAAAGAGAC
+GCTGGAAGGTGTGAAGGACGCTGAGGGTAACGTTGTGGTACACGGTATTTTTGCCAGCGTACCGTACTGC
+ATTCAGTTGCTGGAAGGGCCATACGTTGAAACGGCACCGGAAGTGGTTGCAGCATTCAGACCGAAGAGTG
+CAAGACGCGACGTTAGCGAATAAAAAAATCCCCCCGAGCGGGGGGATCTCAAAACAATTAGTGGGATTCA
+CCAATCGGCAGAACGGTGCGACCAAACTGCTCGTTCAGTACTTCACCCATCGCCAGATAGATTGCGCTGG
+CACCGCAGATCAGCCCAATCCAGCCGGCAAAGTGGATGATTGCGGCGTTACCGGCAATGTTACCGATCGC
+CAGCAGGGCAAACAGCACGGTCAGGCTAAAGAAAACGAATTGCAGAACGCGTGCGCCTTTCAGCGTGCCG
+AAGAACATAAACAGCGTAAATACGCCCCACAGACCCAGGTAGACACCAAGGAACTGTGCATTTGGCGCAT
+CGGTCAGACCCAGTTTCGGCATCAGCAGAATCGCAACCAGCGTCAGCCAGAAAGAACCGTAAGAGGTGAA
+TGCGGTTAAACCGAAAGTGTTGCCTTTTTTGTACTCCAGCAGACCAGCAAAAATTTGCGCGATGCCGCCG
+TAGAAAATGCCCATGGCAAGAATAATACCGTCCAGAGCGAAATAACCCACGTTGTGCAGGTTAAGCAGAA
+TGGTGGTCATGCCGAAGCCCATCAGGCCCAGCGGTGCCGGATTAGCCAACTTAGTGTTGCCCATAATTCC
+TCAAAAATCATCATCGAATGAATGGTGAAATAATTTCCCTGAATAACTGTAGTGTTTTCAGGGCGCGGCA
+TAATAATCAGCCAGTGGGGCAGTGTC
+>gi|1786192|gb|AE000112|ECAE000112 Escherichia coli , htgA, yaaI, dnaK, dnaJ, yi81_1, yi82_1, gefL, nhaA, nhaR, insB_1, insA_1 genes from bases 10539 to 20717 (section 2 of 400) of the complete genome
+CTGAATAACTGTAGTGTTTTCAGGGCGCGGCATAATAATCAGCCAGTGGGGCAGTGTCTACGATCTTTTG
+AGGGGAAAATGAAAATTTTCCCCGGTTTCCGGTATCAGACCTGAGTGGCGCTAACCATCCGGCGCAGGCA
+GGCGATTTGCAGTACGGCTGGAATCGTCACGCGATAGGCGCTGCCGCTGACCGCTTTAACCCCATTTAGT
+GCCGCACCTACAGGGCCTCCCAGCCCCGCGCCGCGCAGCAAACCATGCCCAAGTACGCTCATTGCTGCGT
+GGGTGCGTAAAATGCGGGTCAGTTGGCTGGAAAGCAAATGCGACACACCTTTTGCCAATAATTTGTCTTT
+CATCAGCAGCGGCAGCAGCTCTTCCAGCTCATTCACCCTGGCATCGACCGCGTGCAGAAACTCCTGCTTA
+TGTTCCTCGTCCATTTTCTTCCAGGTATTACGCAGAAATTGTTCCAGTAACTGTTGCTCAATTTCAAACG
+TAGACATCTCTTTGTCGGCTTTCAGCTTCAATCGCTTTGAAACATCGAGCAAAATGGCCCGATACAATTT
+ACCGTGTCCGCGCAGTTTGTTGGCGATACTATCGCCACCAAAATGCTGTAATTCTCCGGCAATCAGCTGC
+CAGTTGCGGCGATGTTGCTCGGGATGCCCTTCCATCGATTTAAACAGTTCGTTGCGCATCAGTACGCTGG
+AGAGGCGAGTTTTGCCTTTTTCATTATGGGTGAGCAATCGGGCGAAATTTGCCAACTGTTCCTCACTACA
+ATGCTGAAGAAAATCCAGATCTGAATCATTCAGGTAATTAACATTCATTTTTTGTGGCTTCTATATTCTG
+GCGTTAGTCGTCGCCGATAATTTTCAGCGTGGCCATATCCGATGAGTTCACCGTATGACCCGAAAAGGTG
+ATTTTTGAGACGCAGCGTTTATTGTCGTTATCGCTGTTAATGTTGATCCAGTCAGTGGTTTGCCCTTCTT
+TTATTTCTGAAGGAATATTCAGGCTCTGACTGGCGCTACGGGCGGCTTTGAAATAAACCGATGCACCGCT
+TAACTGTAAATCGCCATGGTCGGCAGAGAGTTGTATGCGTTTCACAATGCGACAAACAGGAAGTTTCAGC
+GCCAGATCGTTGGTTTCGTTACGCGGCATTGCAATGGCGCCGAGGAGTTTATGGTCGTTTGCCTGCGCCG
+TGCAGCACAGCATCAGGCTAATCGCCAGGCTGGCGGAAATCGTAAAAACGGATTTCATAAGGATTCTCTT
+AGTGGGAAGAGGTAGGGGGATGAATACCCACTAGTTTACTGCTGATAAAGAGAAGATTCAGGCACGTAAT
+CTTTTCTTTTTATTACAATTTTTTGATGAATGCCTTGGCTGCGATTCATTCTTTATATGAATAAAATTGC
+TGTCAATTTTACGTCTTGTCCTGCCATATCGCGAAATTTCTGCGCAAAAGCACAAAAAATTTTTGCATCT
+CCCCCTTGATGACGTGGTTTACGACCCCATTTAGTAGTCAACCGCAGTGAGTGAGTCTGCAAAAAAATGA
+AATTGGGCAGTTGAAACCAGACGTTTCGCCCCTATTACAGACTCACAACCACATGATGACCGAATATATA
+GTGGAGACGTTTAGATGGGTAAAATAATTGGTATCGACCTGGGTACTACCAACTCTTGTGTAGCGATTAT
+GGATGGCACCACTCCTCGCGTGCTGGAGAACGCCGAAGGCGATCGCACCACGCCTTCTATCATTGCCTAT
+ACCCAGGATGGTGAAACTCTAGTTGGTCAGCCGGCTAAACGTCAGGCAGTGACGAACCCGCAAAACACTC
+TGTTTGCGATTAAACGCCTGATTGGTCGCCGCTTCCAGGACGAAGAAGTACAGCGTGATGTTTCCATCAT
+GCCGTTCAAAATTATTGCTGCTGATAACGGCGACGCATGGGTCGAAGTTAAAGGCCAGAAAATGGCACCG
+CCGCAGATTTCTGCTGAAGTGCTGAAAAAAATGAAGAAAACCGCTGAAGATTACCTGGGTGAACCGGTAA
+CTGAAGCTGTTATCACCGTACCGGCATACTTTAACGATGCTCAGCGTCAGGCAACCAAAGACGCAGGCCG
+TATCGCTGGTCTGGAAGTAAAACGTATCATCAACGAACCGACCGCAGCTGCGCTGGCTTACGGTCTGGAC
+AAAGGCACTGGCAACCGTACTATCGCGGTTTATGACCTGGGTGGTGGTACTTTCGATATTTCTATTATCG
+AAATCGACGAAGTTGACGGCGAAAAAACCTTCGAAGTTCTGGCAACCAACGGTGATACCCACCTGGGGGG
+TGAAGACTTCGACAGCCGTCTGATCAACTATCTGGTTGAAGAATTCAAGAAAGATCAGGGCATTGACCTG
+CGCAACGATCCGCTGGCAATGCAGCGCCTGAAAGAAGCGGCAGAAAAAGCGAAAATCGAACTGTCTTCCG
+CTCAGCAGACCGACGTTAACCTGCCATACATCACTGCAGACGCGACCGGTCCGAAACACATGAACATCAA
+AGTGACTCGTGCGAAACTGGAAAGCCTGGTTGAAGATCTGGTAAACCGTTCCATTGAGCCGCTGAAAGTT
+GCACTGCAGGACGCTGGCCTGTCCGTATCTGATATCGACGACGTTATCCTCGTTGGTGGTCAGACTCGTA
+TGCCAATGGTTCAGAAGAAAGTTGCTGAGTTCTTTGGTAAAGAGCCGCGTAAAGACGTTAACCCGGACGA
+AGCTGTAGCAATCGGTGCTGCTGTTCAGGGTGGTGTTCTGACTGGTGACGTAAAAGACGTACTGCTGCTG
+GACGTTACCCCGCTGTCTCTGGGTATCGAAACCATGGGCGGTGTGATGACGACGCTGATCGCGAAAAACA
+CCACTATCCCGACCAAGCACAGCCAGGTGTTCTCTACCGCTGAAGACAACCAGTCTGCGGTAACCATCCA
+TGTGCTGCAGGGTGAACGTAAACGTGCGGCTGATAACAAATCTCTGGGTCAGTTCAACCTAGATGGTATC
+AACCCGGCACCGCGCGGCATGCCGCAGATCGAAGTTACCTTCGATATCGATGCTGACGGTATCCTGCACG
+TTTCCGCGAAAGATAAAAACAGCGGTAAAGAGCAGAAGATCACCATCAAGGCTTCTTCTGGTCTGAACGA
+AGATGAAATCCAGAAAATGGTACGCGACGCAGAAGCTAACGCCGAAGCTGACCGTAAGTTTGAAGAGCTG
+GTACAGACTCGCAACCAGGGCGACCATCTGCTGCACAGCACCCGTAAGCAGGTTGAAGAAGCAGGCGACA
+AACTGCCGGCTGACGACAAAACTGCTATCGAGTCTGCGCTGACTGCACTGGAAACTGCTCTGAAAGGTGA
+AGACAAAGCCGCTATCGAAGCGAAAATGCAGGAACTGGCACAGGTTTCCCAGAAACTGATGGAAATCGCC
+CAGCAGCAACATGCCCAGCAGCAGACTGCCGGTGCTGATGCTTCTGCAAACAACGCGAAAGATGACGATG
+TTGTCGACGCTGAATTTGAAGAAGTCAAAGACAAAAAATAATCGCCCTATAAACGGGTAATTATACTGAC
+ACGGGCGAAGGGGAATTTCCTCTCCGCCCGTGCATTCATCTAGGGGCAATTTAAAAAAGATGGCTAAGCA
+AGATTATTACGAGATTTTAGGCGTTTCCAAAACAGCGGAAGAGCGTGAAATCAGAAAGGCCTACAAACGC
+CTGGCCATGAAATACCACCCGGACCGTAACCAGGGTGACAAAGAGGCCGAGGCGAAATTTAAAGAGATCA
+AGGAAGCTTATGAAGTTCTGACCGACTCGCAAAAACGTGCGGCATACGATCAGTATGGTCATGCTGCGTT
+TGAGCAAGGTGGCATGGGCGGCGGCGGTTTTGGCGGCGGCGCAGACTTCAGCGATATTTTTGGTGACGTT
+TTCGGCGATATTTTTGGCGGCGGACGTGGTCGTCAACGTGCGGCGCGCGGTGCTGATTTACGCTATAACA
+TGGAGCTCACCCTCGAAGAAGCTGTACGTGGCGTGACCAAAGAGATCCGCATTCCGACTCTGGAAGAGTG
+TGACGTTTGCCACGGTAGCGGTGCAAAACCAGGTACACAGCCGCAGACTTGTCCGACCTGTCATGGTTCT
+GGTCAGGTGCAGATGCGCCAGGGATTCTTCGCTGTACAGCAGACCTGTCCACACTGTCAGGGCCGCGGTA
+CGCTGATCAAAGATCCGTGCAACAAATGTCATGGTCATGGTCGTGTTGAGCGCAGCAAAACGCTGTCCGT
+TAAAATCCCGGCAGGGGTGGACACTGGAGACCGCATCCGTCTTGCGGGCGAAGGTGAAGCGGGCGAGCAT
+GGCGCACCGGCAGGCGATCTGTACGTTCAGGTTCAGGTTAAACAGCACCCGATTTTCGAGCGTGAAGGCA
+ACAACCTGTATTGCGAAGTCCCGATCAACTTCGCTATGGCGGCGCTGGGTGGCGAAATCGAAGTACCGAC
+CCTTGATGGTCGCGTCAAACTGAAAGTGCCTGGCGAAACCCAGACCGGTAAGCTATTCCGTATGCGCGGT
+AAAGGCGTCAAGTCTGTCCGCGGTGGCGCACAGGGTGATTTGCTGTGCCGCGTTGTCGTCGAAACACCGG
+TAGGCCTGAACGAAAGGCAGAAACAGCTGCTGCAAGAGCTGCAAGAAAGCTTCGGTGGCCCAACCGGCGA
+GCACAACAGCCCGCGCTCAAAGAGCTTCTTTGATGGTGTGAAGAAGTTTTTTGACGACCTGACCCGCTAA
+CCTCCCCAAAAGCCTGCCCGTGGGCAGGCCTGGGTAAAAATAGGGTGCGTTGAAGATATGCGAGCACCTG
+TAAAGTGGCGGGGATCACTCCCATAAGCGCTAACTTAAGGGTTGTGGTATTACGCCTGATATGATTTAAC
+GTGCCGATGAATTACTCTCACGATAACTGGTCAGCAATTCTGGCCCATATTGGTAAGCCCGAAGAACTGG
+ATACTTCGGCACGTAATGCCGGGGCTCTAACCCGCCGCCGCGAAATTCGTGATGCTGCAACTCTGCTACG
+TCTGGGGCTGGCTTACGGCCCCGGGGGGATGTCATTACGTGAAGTCACTGCATGGGCTCAGCTCCATGAC
+GTTGCAACATTATCTGACGTGGCTCTCCTGAAGCGGCTGCGGAATGCCGCCGACTGGTTTGGCATACTTG
+CCGCACAAACACTTGCTGTACGCGCCGCAGTTACGGGTTGTACAAGCGGAAAGAGATTGCGTCTTGTCGA
+TGGAACAGCAATCAGTGCGCCCGGGGGCGGCAGCGCTGAATGGCGACTACATATGGGATATGATCCTCAT
+ACCTGTCAGTTCACTGATTTTGAGCTAACCGACAGCAGAGACGCTGAACGGCTGGACCGATTTGCGCAAA
+CGGCAGACGAGATACGCATTGCTGACCGGGGATTCGGTTCGCGTCCCGAATGTATCCGCTCACTTGCTTT
+TGGAGAAGCTGATTATATCGTCCGGGTTCACTGGCGAGGATTGCGCTGGTTAACTGCAGAAGGAATGCGC
+TTTGACATGATGGGTTTTCTGCGCGGGCTGGATTGCGGTAAGAACGGTGAAACCACTGTAATGATAGGCA
+ATTCAGGTAATAAAAAAGCCGGAGCTCCCTTTCCGGCACGTCTCATTGCCGTATCACTTCCTCCCGAAAA
+AGCATTAATCAGTAAAACCCGACTGCTCAGCGAGAATCGTCGAAAAGGACGAGTAGTTCAGGCGGAAACG
+CTGGAAGCAGCGGGCCATGTGCTATTGCTAACATCATTACCGGAAGATGAATATTCAGCAGAGCAAGTGG
+CTGATTGTTACCGTCTGCGATGGCAAATTGAACTGGCTTTTAAGCGGCTCAAAAGTTTGCTGCACCTGGA
+TGCTTTGCGTGCAAAGGAACCTGAACTCGCGAAAGCGTGGATATTTGCTAATCTACTCGCCGCATTTTTA
+ATTGACGACATAATCCAGCCATCGCTGGATTTCCCCCCCAGAAGTGCCGGATCCGAAAAGAAGAACTAAC
+TCGTTGTGGAGAATAACAAAAATGGTCATCTGGAGCTTACAGGTGGCCATTCGTGGGACAGTATCCCTGA
+CAGCCTACAAAACGCAATTGAAGAACGCGAGGCATCGTCTTAACGAGGCACCGAGGCGTCGCATTCTTCA
+GATGGTTCAACCCTTAAGTTAGCGCTTATGGGATCACTCCCCGCCGTTGCTCTTACTCGGATTCGTAAGC
+CGTGAAAACAGCAACCTCCGTCTGGCCAGTTCGGATGTGAACCTCACAGAGGTCTTTTCTCGTTACCAGC
+GCCGCCACTACGGCGGTGATACAGATGACGATCAGGGCGACAATCATCGCCTTATGCTGCTTCATTGCTC
+TCTTCTCCTTGACCTTACGGTCAGTAAGAGGCACTCTACATGTGTTCAGCATATAGGAGGCCTCGGGTTG
+ATGGTAAAATATCACTCGGGGCTTTTCTCTATCTGCCGTTCAGCTAATGCCTGAGACAGACAGCCTCAAG
+CACCCGCCGCTATTATATCGCTCTCTTTAACCCATTTTGTTTTATCGATTCTAATCCTGAAGACGCCTCG
+CATTTTTGTGGCGTAATTTTTTAATGATTTAATTATTTAACTTTAATTTATCTCTTCATCGCAATTATTG
+ACGACAAGCTGGATTATTTTTGAAATATTGGCCTAACAAGCATCGCCGACTGACAACAAATTAATTATTA
+CTTTTCCTAATTAATCCCTCAGGAATCCTCACCTTAAGCTATGATTATCTAGGCTTAGGGTCACTCGTGA
+GCGCTTACAGCCGTCAAAAACGCATCTCACCGCTGATGGCGCAAATTCTTCAATAGCTCGTAAAAAACGA
+ATTATTCCTACACTATAATCTGATTTTAACGATGATTCGTGCGGGGTAAAATAGTAAAAACGATCTATTC
+ACCTGAAAGAGAAATAAAAAGTGAAACATCTGCATCGATTCTTTAGCAGTGATGCCTCGGGAGGCATTAT
+TCTTATCATTGCCGCTATCCTGGCGATGATTATGGCCAACAGCGGCGCAACCAGTGGATGGTATCACGAC
+TTTCTGGAGACGCCGGTTCAGCTCCGGGTTGGTTCACTCGAAATCAACAAAAACATGCTGTTATGGATAA
+ATGACGCGCTGATGGCGGTATTTTTCCTGTTAGTCGGTCTGGAAGTTAAACGTGAACTGATGCAAGGATC
+GCTAGCCAGCTTACGCCAGGCCGCATTTCCAGTTATCGCCGCTATTGGTGGGATGATTGTGCCGGCATTA
+CTCTATCTGGCTTTTAACTATGCCGATCCGATTACCCGCGAAGGGTGGGCGATCCCGGCGGCTACTGACA
+TTGCTTTTGCACTTGGTGTACTGGCGCTGTTGGGAAGTCGTGTTCCGTTAGCGCTGAAGATCTTTTTGAT
+GGCTCTGGCTATTATCGACGATCTTGGGGCCATCATTATCATCGCATTGTTCTACACTAATGACTTATCG
+ATGGCCTCTCTTGGCGTCGCGGCTGTAGCAATTGCGGTACTCGCGGTATTGAATCTGTGTGGTGCACGCC
+GCACGGGCGTCTATATTCTTGTTGGCGTGGTGTTGTGGACTGCGGTGTTGAAATCGGGGGTTCACGCAAC
+TCTGGCGGGGGTAATTGTCGGCTTCTTTATTCCTTTGAAAGAGAAGCATGGGCGTTCTCCAGCGAAGCGA
+CTGGAGCATGTGTTGCACCCGTGGGTGGCGTATCTGATTTTGCCGCTGTTTGCATTTGCTAATGCTGGCG
+TTTCACTGCAAGGCGTCACGCTGGATGGCTTGACCTCCATTCTGCCATTGGGGATCATCGCTGGCTTGCT
+GATTGGCAAACCGCTGGGGATTAGTCTGTTCTGCTGGTTGGCGCTGCGTTTGAAACTGGCGCATCTGCCT
+GAGGGAACGACTTATCAGCAAATTATGGTGGTGGGGATCCTGTGCGGTATCGGTTTTACTATGTCTATCT
+TTATTGCCAGCCTGGCCTTTGGTAGCGTAGATCCAGAACTGATTAACTGGGCGAAACTCGGTATCCTGGT
+CGGTTCTATCTCTTCGGCGGTAATTGGATACAGCTGGTTACGCGTTCGTTTGCGTCCATCAGTTTGACAG
+GACGGTTTACCGGGGAGCCATAAACGGCTCCCTTTTCATTGTTATCAGGGAGAGAAATGAGCATGTCTCA
+TATCAATTACAACCACTTGTATTACTTCTGGCATGTCTATAAAGAAGGTTCCGTGGTTGGCGCAGCGGAG
+GCGCTTTATTTAACTCCACAAACCATTACCGGACAGATTCGAGCGCTGGAAGAGCGCCTGCAAGGCAAAT
+TATTTAAACGCAAGGGACGTGGTCTCGAACCCAGCGAGCTGGGAGAACTGGTCTATCGCTATGCCGATAA
+AATGTTCACCTTAAGCCAGGAAATGCTGGATATTGTGAACTATCGCAAAGAATCCAATTTATTGTTTGAC
+GTTGGCGTGGCTGATGCACTTTCCAAACGCCTGGTCAGTAGCGTACTTAACGCCGCAGTGGTAGAAGGCG
+AGCCCATTCATCTTCGCTGCTTCGAATCCACCCACGAAATGCTGCTGGAGCAATTAAGTCAGCATAAACT
+GGATATGATCATTTCTGACTGTCCGATAGACTCTACGCAGCAGGAAGGCCTGTTCTCCGTGAGAATTGGC
+GAATGTGGCGTGAGTTTCTGGTGTACAAATCCACCACCAGAAAAACCGTTCCCGGCTTGTCTGGAAGAAC
+GGCGACTTTTGATTCCTGGGCGACGTTCAATGTTAGGGCGCAAATTGCTTAACTGGTTTAACTCCCAGGG
+ATTAAACGTAGAAATCCTCGGCGAGTTTGATGATGCCGCTTTGATGAAAGCTTTTGGTGCGATGCACAAT
+GCAATCTTCGTTGCCCCAACGCTTTATGCATATGACTTTTATGCCGATAAAACTGTCGTAGAAATTGGTC
+GCGTCGAGAATGTGATGGAAGAGTACCATGCTATTTTTGCTGAGCGGATGATTCAGCACCCGGCGGTACA
+GCGAATCTGCAATACGGATTATTCTGCGCTTTTTAGTCCAGCGGTGCGTTAATCGGCAGCTCCCCCAAAG
+TTAAGGTGGGGGAGATAGATTAGTTGTACATTACCACGATTTTGACTCGGCTCATTATTTGCCCGCTTGA
+GACATTGTTTCCATATGTACGCGGGCGAATAAATAGAGGAATCTGATTACTTCCTTCATGGGGATGCTGA
+AAAGAGTAGTAATTGCTGGTAATGACTCCAACTTATTGATAGTGTTTTATGTTCAGATAATGCCCGATGA
+CTTTGTCATGCAGCTCCACCGATTTTGAGAACGACAGCGACTTCCGTCCCAGCCGTGCCAGGTGCTGCCT
+CAGATTCAGGTTATGCCGCTCAATTCGCTGCGTATATCGCTTGCTGATTACGTGCAGCTTTCCCTTCAGG
+CGGGATTCATACAGCGGCCAGCCATCCGTCATCCATATCACCACGTCAAAGGGTGACAGCAGGCTCATAA
+GACGCCCCAGCGTCGCCATAGTGCGTTCACCGAATACGTGCGCAACAACCGTCTTCCGGAGACTGTCATA
+CGCGTAAAACAGCCAGCGCTGGCGCGATTTAGCCCCGACATAGCCCCACTGTTCGTCCATTTCCGCGCAG
+ACGATGACGTCACTGCCCGGCTGTATGCGCGAGGTTACCGACTGCGGCCTGAGTTTTTTAAGTGACGTAA
+AATCGTGTTGAGGCCAACGCCCATAATGCGGGCTGTTGCCCGGCATCCAACGCCATTCATGGCCATATCA
+ATGATTTTCTGGTGCGTACCGGGTTGAGAAGCGGTGTAAGTGAACTGCAGTTGCCATGTTTTACGGCAGT
+GAGAGCAGAGATAGCGCTGATGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGTAGCTGAACA
+GGAGGGACAGCTGATAGAAACAGAAGCCACTGGAGCACCTCAAAAACACCATCATACACTAAATCAGTAA
+GTTGGCAGCATCACCTACCTCAATGTGTATCACAATATCCATATTCTTTGTGGGGGAGTCTGGAGATTGA
+GTAGATATTCTTGTTCAGAATGTATCAGCCGATGGTTCTACGATTCTTAAGCCACGAAGAGTTCAGATAG
+TACAACGGCATGTCTCTTTTGACTATCTG
+>gi|1786217|gb|AE000114|ECAE000114 Escherichia coli , caiF, caiE, caiD, caiC, caiB, caiA, caiT, fixA, fixB, fixC, fixX, yaaU genes from bases 34087 to 47220 (section 4 of 400) of the complete genome
+TAATACGGTTCTCTGATGAGGACCGTTTTTTTTTGCCCATTAAGTAAATCTTTTGGGGAATCGATATTTT
+TGATGACATAAGCAGGATTTAGCTCACACTTATCGACGGTGAAGTTGCATACTATCGATATATCCACAAT
+TTTAATATGGCCTTGTTTAATTGCTTCAAAACGAGTCATAGCCAGACTTTTAATTTGTGAAACTGGAGTT
+CGTATGTGTGAAGGATATGTTGAAAAACCACTCTACTTGTTAATCGCCGAATGGATGATGGCTGAAAATC
+GGTGGGTGATAGCAAGAGAGATCTCTATTCATTTCGATATTGAACACAGCAAGGCGGTTAATACCCTGAC
+TTATATTCTGTCGGAAGTCACAGAAATAAGCTGCGAAGTTAAGATGATCCCTAATAAGCTGGAAGGGCGG
+GGATGCCAGTGTCAGCGACTGGTTAAAGTGGTCGATATCGATGAGCAAATTTACGCGCGCCTGCGCAATA
+ACAGTCGGGAAAAATTAGTCGGTGTAAGAAAGACGCCGCGTATTCCTGCCGTTCCGCTCACGGAACTTAA
+CCGCGAGCAGAAGTGGCAGATGATGTTGTCAAAGAGTATGCGTCGTTAATTTTATCTCGTTGATACCGGG
+CGTCCTGCTTGCCAGATGCGATGTTGTAGCATCTTATCCAGCAACCAGGTCGCATCCGGCAAGATCACCG
+TTTAGGCGTCACATCCGTCGTCCCCTGCAAACGGGGGCGATTTTCCTCCATTTGCCTCAGTGGCTGCGTT
+TCATGTAACGATACATGACAGCGCCCGACAAGATCCTGATACTCTTTGGTATTCAACCGTTTCCAGTGTA
+ACTCGTCGTCACTAACATTGCGTACAGCGCGGGCTGGCGTACCCATCAACAACTGGCGTTTCTCGCCGCG
+AAAGCCCGCTTTGACAAAGCTCATGGCGGCAACAATGCTCTCTTCGCCAATGACCGCGCCATCCATAATC
+ACGCTGTTCATCCCGACCAATGCATCGCGACCAATCAAACAACCATGCAGGATCGCTCCGTGCCCGATAT
+GGCCGTTTTCCCCAACGATAGTGTCAGTGTCGCAGTAGCCATGCATAATGCAGCCATCCTGAATATTGGC
+TCCCGCTTGCACGATCAACCGCCCGTAGTCACCACGCAGTGAGGCGAGTGGGCCGATGTAGACACCGGCT
+CCCACAATCACATCGCCAATCAAGACGGCACTGGGATGGACAAACGCCGTCGGGTGAACCACCGGAATTA
+ACCCCTCAAAGGCGTAATAGCTCACGGTTGTTAACGTCCTTTCCACACCGGATCGCGCTTCTCGGCAAAC
+GCCAGCGGCCCTTCAATGGCATCTTCCGAATGCAGAACCGATGGATAGTGTTTCAACACGCCGCTGCGAA
+TATAGCGATACGCTTCTTCTACCGGCATTTCGCTGGTGGTGCGGTAGATCTCTTTCAGCGCCGCAATCGC
+CAGCGGGGCGCTGTTAACCAGCTGCTGAGCCAGTTCGCGGGCGTTATCCATCAGTTCCGCCTGGCTAACC
+ACGCGGTTGACTATCCCCCAACGCAGCGCCTCTTCTGCGCCCATTCGTCTGCCGGTCATCACCATTTCAT
+TGACGATGGCAGGCGGCAGGATCTTCGGCAGACGCAGCACACCGCCGCTGTCAGGAACGATGCCCAGTTT
+GGCTTCCGGCAGGGCGAAGCTGGCGTTATCGGCACAAACAATAAAATCTGCCGCCAGCGCCAGTTCAAAG
+CCGCCGCCAAAGGCATAGCCGTTCACAGCTGCGATAACCGGTTTGTCGAGATTGAAAATTTCGGTTAATC
+CCGCAAAACCACCCGGACCAAAGTCAGCATCCGGTGCTTCGCCTTCTGCTGCCGCTTTTAAATCCCAGCC
+CGCGGAAAAGAACTTCTCTCCGGCACCGGTAATAATGGCGACACGTAATTGCGGATCGTCACGGAAATTT
+AGAAATACTTCGCCCATTTCAAAGCTGGTTTTTGCATCAATAGCATTCGCTTTTGGACGATCAAGGGTAA
+TTTCCAGAATTGATCCATTGCGGGTCAGATGTAATGATTCACTCATTCCTTTTCTCCATTTTTGCTTTTT
+CAGGGACGACAACATCCCTGCAAAAAATGCATATTGTTTTAGAGTGTGATTATTAGCTGGCAGGGTAGTT
+CCCTGCTGTTTCATTTATTTCAGATTCTTTCTAATTATTTTCCCCGAGCAATTACGTGGCAGATCTTTTC
+TGATCTCCAGATAAGAGGGCACTTTAAATTTCGCCATATTTTGTTCGCAGAAGCGGAAAAATTCCTCTTC
+GCTCAATGTTTCACCTTCATTCAGCACCACAAATGCTTTGATGGCTTCATCGCGAATCGAATCTTTAATA
+CCCACAACCACGATGTCCTGAATTTTCGGGTGCGCGGCGATAATATTTTCCAGCTCCACGCAGGAGACAT
+TCTCGCCGCCACGTTTAATCATATTGCAGCGGCGATCGACGAAATAAAAAAAGTCCTCTTCGTCGCGGTA
+TCCGGTATCGCCGGTATGCAGCCAGCCATCGGCTTCCAGCACTTTCGCAGTGGCTTGTGGGTTGAGAAAG
+TACTCTTTGAAGATGGTTTTCCCAGGTATGCCTTTAATGCAGATTTCACCGATCTCACCAGCCGGGAGCG
+GGCGATTGTGATCGTCGCGGATCTCCGCTTCGTAGCAAAACCCCACCCGACCAATCGACGGCCAGCGTCG
+TTTATCGCCAGGACGATCGCCGATAATGCCCACAATGGTTTCCGTCATCCCATAAGACGTCAGCAAGCGA
+ACGCCGAAGCGTTCACAAAACGCATCTTTTTCCTGCTCCGACAAGTTGAGATAAAACATCACTTCCCGCA
+GGCGGTGTTGCTGATCGTTCGCTGAAGGCGGCTGTACCATCAACGTACGGATCATCATCGGAATACATTC
+GGTAACGGTGGCGCGGTACTTCTGTACCTGTCCCCAGAAGGCGCGGGCGCTGTATTTCTCGACCAGCACA
+AAGGTGGCCCCGGCAGAAAACGCCGCCATCGCCGCAGTACACTGGCAATCGATATGAAACGCAGGCATTA
+CCGTCAGGTAGACGTCATCGTCACGCAGTGCACACTGCCAGGCGGAGTAATATCCAGCGAAGCGCAGGTT
+GTAATGGGTAATCACCACACCTTTCGGTCGGGAGGTGGTGCCGGAGGTGAAGAGAATTTCCGCCGTATCG
+TCAGTCGATAGCGGCGGTGCATAGCACAAGGTGGCAGGTTGTTGATTTTTCAGTTGAGTAAACGAACTCA
+CGCCATCATCAGCGGGAAGTGCCACATCTGTCAGGCAAATGTGCCGCAATTGAGTGGCATCTTCCTGCTG
+AATCTGTTGATACATAGGATAGAATTGCGCACTGGTCACCAGCAGGCACGCCTGGCTATTTTGCAGGATC
+CACGCGCTTTCCTCGCACAACAGGCGGGCGTTAATCGGCACCATAATCGCGCCAATTTTTGCCAGCCCGA
+ACCAGCAAAAGATAAATTCCGGGCAGTTGTCGAGATGTAGTGCAACCTTGTCGCCTTTGCGAATCCCCAG
+CGTATAAAACAGGTTTGCCGTGCGGTTAATCTCCTGATTTAACTCAAGATAACTATACCGGTTAACGACT
+CCGCCGCTGGATTCACAAATCAGCGCCGTTTTATGACCGTAAACGTCCGCAAGATCGTCCCACATTTGAC
+GTAGATGTTGTCCGCCAATGATATCCATTGCACCTCTATCCATTTTTGTTCGTTTGTTATTGGGCGGGCG
+CTAGTCAGGCAAGCCGACTGACGCCACGCGTTTAGTCCTCAACTTTGGCCAGACCTTTGCTGACCAACTC
+CTGAATGTCGTTTTCGCTGTAGCCGATATTTTTCAAAATGGCAGCCGTGTCCATGCCATGTGAGGGCATT
+CCGCGCCAGATTTGTCCGGGGTTATTTTTGAATTTCGGCATGATGTTCGGCCCTTTGCAGGTGCGACCAT
+CCATCGTTTGCCACTGAGTGATTGATTCGCGAGCCACATACTGTGGATTGCTTTCCAGTTCCGGTACGGT
+CAGCACTTTGGCGCAGGCGATATTCAGTTCAGCAAAGCGTTCTTTTACTTCCGCGATGGTATGTGTCGCC
+AGCCAGGCATCGAGTTTCTCTTCAACCAGTGGGCCGTAAGGGCATTCGATACGGTGGATAAGCTGAGTGC
+CTTCCGGGATTTCTGGCGTGCCAAGCAGATGTGCGAGGCCAATATCTTTAAAGCACTCTTCAATTTGGGT
+AATGCCCACCAGTTCCATCACGATGTAGCCGTCGGCACATTTATACAGACCGCAACCGGCGTAGTAGGGA
+TCTTTACCTTTGCTCATGCGCGGGCACATTTCGCCGCCGTTGAAGTAATCCATCATGAAGTACTGGCCCA
+TACGCAGCATCACTTCATACATGGCGATGTCGATACTTTCGCCTTTACCGGTTTCACGCACTTTATGCAG
+TGCTGCCAGCGCCGCCGTGGTGGCGGTCAGGCCAGAAAAGTAATCGGCGGTATACGGGAAGGCAGGCATT
+GGCTGGTCAACATCACCGTTCTGAATCAGGTAACCACTAAAGGCCTGGGCGATAGTGTTATAGGCCGGAA
+GATTGGTGTACTCCTCGGTGCCGTACTGACCAAAACCGGACAGGTGAGCGATAACCAGTTTCGGGTTGTG
+CTGCCACAGTACTTCATCGGTAATGCCACGACGGGCAAAGGCCGGACCTTTACTGGCTTCGATGAAGATA
+TCGGTGGTTTCCATTAATTTCAGAAACGCTTCGCGGCCTTCATCTTTGAAAATATTTAACGACAGCGCGT
+GCAAATTGCGGCGGGAGAGTTGCGGGTAGTTCGGTTGAACGCGAATGGTGTCGGCCCAGGCGACGTTCTC
+GATCCAGATAACTTCCGCGCCCCATTCTGCGAACATTTGCCCGGCAAACGGTCCGGCGATTTCGATACCG
+GAGAAGACAACGCGCAATCCGGCCAACGGCCCGAATTTCGGCATGGGTAGATGATCCATTATTTGCTCCT
+GAAAAATTTATGTAGCGCATGACTGCCGGATGCGGCGTAAACGCTTTATCCGGCCTACATTCGTGCTCCC
+GTAGGCCTGATAAGACGCATCAGCGTCGCATCAGGCAGCGCACGGACTTAGCGGTATTGCTTCAGCACCG
+CACGACCCAGCGTCAGGATCTGCATTTCGTCAGATCCCCCGGAGACGCGGTCTACACGCAGATCACGCCA
+GAAGCGGCTGATGCGGTGGTTGCCCGCAATCCCGACACCGCCCAGCACCTGCATTGCGCTATCCACAACT
+TCAAATGCCGCATTGGCGCAGAAGTATTTGCACATCGCTGCATCGCCAGAGGTGATGGTGCCGTTGTCTG
+CTTTCCACGCTGCTTCATACAGCATGTTTTTCATGGAGTTTAATTTGATCGCCATGTGGGCGAATTTTTC
+CTGAATCAACTGGAAACGACCAATAGCCTCGCCAAACTGCACGCGCTGATTGGCGTAGCGCGCCGCATCT
+TCAAAGGCGCACATCGCCGTACCGTAGTTGGTGAGGGCTACCAGGAAACGTTCATGGTCGAACTCTTCTT
+TGACGCGGTTAAAGCCGTTACCTTCCCGACCGAACATGTCTTTCTCGTCCAGTTCCACGTCGTCAAAGGT
+GATTTCACAGCAGCTATCCATACGCAGACCGAGCTTTTCAAGTTTGGTCACTTTGATGCCCGGTTTGCTC
+ATATCAACAAACCATTCGGTGTAGACAGGTTTGTCCGGAGAAGCCCCGTCGCGCGCCATCACCACGATGT
+ACGGGGTGTAGGCGCTGCTGGTAATAAAACACTTACTACCATTAAGATAAATCTTACCATTTCTACGGGT
+ATAAGTCGTTTTCAGGCTACCCACGTCGGAGCCCGCGCCCGGTTCGGTAATCGCTGAGTTCCACATCTGC
+TTACCGGTGCCGCGGAAAGCCATAATTTTGTCGATCTGCTCTTGTGTGCCTTCGCGCAGGAAGGTGTTGA
+ACCCGCCCGGCAACTGGTACAGCACATAGGTTGGTGCCCCCAGACGTCCCAGCTCCATCCACACGGCGGC
+GAGAGTAACAAACCCCGCGTCCAGACCACCGTGCTCTTCAGGGATCAGCAGACTGTCGATACCCATATCC
+GCCAGTGCTTTGACAAAACGTTCCGGGTAGACGCTGTCACGGTCGCACTCGGCAAAATAGGCCTCCCAGT
+TTTCGCTGGCCATCAGTTCGCGGATACCGGCGACAAACAGTTCCTGCTCATCATTTAAATTAAAATCCAT
+CTTTCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAG
+AGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCA
+GGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAGAATTGACCAACCGATACGCACCAGCAG
+AGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAGGCGTTAACC
+AGCGTAACGGTGGCAATAAAGCAGAGGATGAAGAAGCCCCACATGGTGGCGGTGCTGAGTGGCAGAGCGG
+CCCAGGTTTCAATGATGGCGCGCGCCACACCGTACTGTTCGATCAGATTTGGAATGTTGATGATGTTTTT
+ATCTATCAACAGCAGAGTGTTACTACCGAGTACAGTCCACAGGATCCAGGTTGACGCTGTCAGCCCCAGC
+ACCATGCCGAAGCACAGTTCACGCACAGTACGACCACGGGAGATGCGGGCGAGGAAGATACTCATCTGGA
+TAGCATAAATCACCCACCATGCCCAGTAGAACACGGTCCAGCCCTGCGGGAAGCCGCCTTTAGCGATGGG
+ATCGGTATAGAACAACATGCGCGGCAGATACATCAGCAACATCCCCACCGAATCGGTGAAGTAGTTCATG
+ATGAAGCTGGCACCGCTGACAATGAACACCCAACCCAGCATCAGGAAGCTCAGGTAACTACGCACGTCAC
+TGGCGATACGTACCCCTTTTTGCAGACCGCAAGCGACGCAAATGGCGTTGAGGATAATCCAGCAGGTAAT
+GATGATAGCGTCCAGTTGCAGGGTATGCGGAATGCCAAACAACCATTGCATACACTCGGTCACCAGCGGC
+GTGGCAAGGCCCAGACTGGTACCCATCGCGAAGATCAAGGCGACGAGATAGAAGTTGTCGACGATAGTGC
+CGAACAACCCTTTGGCGTGTTTTTCACCTACCAGCGGCACCAGTGTCGAGCTGGGGCGAATCACTTCCAT
+TTTGCGGACAAAGAAGAAGTAAGCGAAGGCGACTGAAAGGAAGCTGTAAGTGGCCCACGGCAGAGGTCCC
+CAGTGGAACAAGCTGTAAGCCAGCCCCAACTCTTTCGCCCCTGTCGAGTTCGGTTCTAAGCCAAACGGCG
+GGGTGGAGATGTAGTAGTAGATCTCAATCGATCCCCAGAACAGTACGGCAGCAGACGTACAGGAGGCGAA
+CATCATAAAGATCCAACTGGCGGTGCTAAATTCTGGCGGTTCGTTACCTAAACGCTTTTTGGCATACGGG
+CCAAACACCAGCCAGAACCAACCGAAAAGCATCACCACCATATACCATTCAAATGCCCATCCCCATACAT
+TGGTGACGTAACTGAATACAGCATTAATAACGACATTCGCTGCATCCAGATCTCTGACTGTAAGCCAACA
+AAGTATGCCGACGATTATTAACGGCGGAAAGAAAACCTTCGGTTCTATTCCCGTTTTTCTCTTTTCATTC
+TTCATGAGTTAATTCCACTGTGAAAACGAATATTTATTTTGCGTTCCCGTTTGTTTTATTTTTGTTAACA
+TTTAATATAATTATTATTAACCTCGTGGACGCGTTAATGGCTAACTCATAATGGGTATTCAATAAGCTGT
+ATTCTGTGATTGGTATCACATTTTTGTTTCGGGTGAATAGAGGGCGTTTTTTCGTTAATTTTGATTAATA
+ATCAGTTTGTTATGCTCTGTTGTGAGTAAAAAATAACATCTGACTTTCAATATTGGTGATCCATAAAACA
+ATATTGAAAATTTCTTTTTGCTACGCCGTGTTTTCAATATTGGTGAGGAACTTAACAATATTGAAAGTTG
+GATTTATCTGCGTGTGACATTTTCAATATTGGTGATTAAAGTTTTATTTCAAAATTAAAGGGCGTGATAT
+CTGTAATTAACACCACCGATATGAACGACGTTTCCTTCATGATTTCTGGAGATGCAATGAAGATTATTAC
+TTGCTATAAGTGCGTGCCTGATGAACAGGATATTGCGGTCAATAATGCTGATGGTTCATTAGACTTCAGC
+AAAGCCGATGCCAAAATAAGCCAATACGATCTCAACGCTATTGAAGCGGCTTGCCAGCTAAAGCAACAGG
+CAGCAGAGGCGCAGGTGACAGCCTTAAGTGTGGGCGGTAAAGCCCTGACCAACGCCAAAGGGCGTAAAGA
+TGTGCTATCGCGCGGCCCGGATGAACTGATTGTGGTGATTGATGACCAGTTCGAGCAGGCACTGCCGCAA
+CAAACGGCGAGCGCACTGGCTGCAGCCGCCCAGAAAGCAGGCTTTGATCTGATCCTCTGTGGCGATGGTT
+CTTCCGACCTTTATGCCCAGCAGGTTGGTCTGCTGGTGGGCGAAATCCTCAATATTCCGGCAGTTAACGG
+CGTCAGCAAAATTATCTCCCTGACGGCAGATACCCTCACCGTTGAGCGCGAACTGGAAGATGAAACCGAA
+ACCTTAAGCATTCCGCTGCCTGCGGTTGTTGCTGTTTCCACTGATATCAACTCCCCACAAATTCCTTCGA
+TGAAAGCCATTCTCGGCGCGGCGAAAAAGCCCGTCCAGGTATGGTCGGCGGCGGATATTGGTTTTAACGC
+AGAGGCAGCCTGGTCAGAACAACAGGTTGCCGCGCCGAAACAGCGCGAACGTCAGCGCATCGTGATTGAA
+GGCGACGGCGAAGAACAGATCGCCGCATTTGCTGAAAATCTTCGCAAAGTCATTTAATTACAGGGGATGC
+TATGAACACGTTTTCTCAAGTCTGGGTATTCAGCGATACCCCTTCTCGTCTGCCGGAACTGATGAACGGT
+GCGCAGGCTTTAGCTAATCAAATCAACACCTTTGTCCTCAATGATGCCGACGGCGCACAGGCAATCCAGC
+TCGGCGCTAATCATGTCTGGAAATTAAACGGCAAACCGGACGATCGGATGATCGAAGATTACGCCGGTGT
+CATGGCTGACACTATTCGCCAGCACGGCGCAGACGGCCTGGTGCTGCTGCCAAACACCCGTCGCGGCAAA
+TTACTGGCGGCAAAACTGGGTTATCGCCTTAAAGCGGCGGTGTCTAACGATGCCAGCACCGTCAGCGTAC
+AGGACGGTAAAGCGACAGTGAAACACATGGTTTACGGTGGTCTGGCGATTGGCGAAGAACGCATTGCCAC
+GCCGTATGCGGTACTGACCATCAGCAGCGGCACGTTCGATGCGGCTCAGCCAGACGCGTCACGCACTGGC
+GAAACGCACACCGTGGAGTGGCAGGCTCCGGCTGTGGCGATTACCCGCACGGCAACCCAGGCGCGCCAGA
+GCAACAGCGTCGATCTCGACAAAGCCCGTCTGGTGGTCAGCGTCGGTCGCGGTATTGGCAGCAAAGAGAA
+CATTGCGCTGGCAGAACAGCTTTGCAAGGCGATAGGTGCGGAGTTGGCCTGTTCTCGTCCGGTGGCGGAA
+AACGAAAAATGGATGGAGCACGAACGCTATGTCGGTATCTCCAACCTGATGCTGAAACCTGAACTGTACC
+TGGCGGTGGGGATCTCCGGGCAGATCCAGCACATGGTTGGCGCTAACGCGTCGCAAACCATTTTCGCCAT
+CAATAAAGATAAAAATGCGCCGATCTTCCAGTACGCGGATTACGGCATTGTTGGCGACGCCGTGAAGATC
+CTTCCGGCGCTGACCGCAGCTTTAGCGCGTTGATCCACTCTGGCAGGGCTGCATTTTGGCCCTGCCGCTG
+ACAGGGAGCTCTTATGTCCGAAGATATCTTTGACGCCATCATCGTCGGTGCAGGGCTTGCCGGTTCGGTT
+GCCGCACTGGTGCTCGCCCGCGAAGGTGCGCAAGTGTTAGTTATCGAGCGTGGCAATTCCGCAGGTGCCA
+AGAACGTCACCGGCGGGCGTCTCTATGCCCACAGTCTGGAACACATTATTCCTGGTTTCGCCGACTCCGC
+CCCCGTAGAACGCCTGATCACCCATGAAAAACTCGCGTTTATGACGGAAAAGTCAGCGATGACTATGGAC
+TACTGCAATGGTGACGAAACCTCGCCATCCCAGCGTTCTTACTCCGTTTTGCGCAGTAAATTTGATGCCT
+GGCTGATGGAGCAGGCCGAAGAAGCGGGCGCGCAGTTAATTACCGGGATCCGCGTCGATAACCTCGTACA
+GCGCGATGGCAAAGTCGTCGGTGTAGAAGCCGATGGCGATGTGATTGAAGCGAAAACGGTGATCCTTGCT
+GATGGGGTGAACTCCATCCTTGCCGAAAAATTGGGGATGGCAAAACGCGTCAAACCGACGGATGTGGCGG
+TTGGCGTGAAGGAACTGATCGAGTTACCGAAGTCGGTTATTGAAGACCGTTTTCAGTTGCAGGGTAATCA
+GGGGGCGGCTTGCCTGTTTGCGGGATCACCCACCGATGGCCTGATGGGCGGCGGCTTCCTTTATACCAAT
+GAAAACACCCTGTCGCTGGGGCTGGTTTGTGGTTTGCATCATCTGCATGACGCGAAAAAATCGGTGCCGC
+AAATGCTGGAAGATTTCAAACAGCATCCGGCCGTTGCACCGCTGATCGCGGGCGGCAAGCTGGTGGAATA
+TTCCGCTCACGTAGTGCCGGAAGCAGGCATCAACATGCTGCCGGAGTTGGTTGGTGACGGCGTATTGATT
+GCCGGTGATGCCGCCGGAATGTGTATGAACCTCGGTTTTACCATTCGCGGTATGGATCTGGCGATTGCCG
+CCGGGGAAGCCGCAGCAAAAACCGTGCTTTCAGCGATGAAAAGCGACGATTTCAGTAAGCAAAAACTGGC
+GGAATATCGTCAGCATCTTGAGAGTGGTCCGCTGCGCGATATGCGTATGTACCAGAAACTACCGGCGTTC
+CTTGATAACCCACGCATGTTTAGCGGCTACCCGGAGCTGGCGGTGGGTGTGGCGCGTGACCTGTTCACCA
+TTGATGGCAGCGCGCCGGAACTGATGCGCAAGAAAATCCTCCGCCACGGCAAGAAAGTGGGCTTCATCAA
+TCTAATCAAGGATGGCATGAAAGGAGTGACCGTTTTATGACTTCTCCCGTCAATGTGGACGTCAAACTGG
+GCGTCAATAAATTCAATGTCGATGAAGAGCATCCGCACATTGTTGTGAAGGCCGATGCTGATAAACAGGC
+GCTGGAGCTGCTGGTGAAAGCGTGCCCCGCAGGTCTGTACAAGAAGCAGGATGACGGCAGTGTGCGCTTC
+GATTACGCCGGATGTCTGGAGTGCGGCACCTGTCGCATTCTGGGGCTGGGGTCGGCGCTGGAACAGTGGG
+AATACCCGCGCGGCACCTTTGGTGTGGAGTTCCGTTACGGCTGATGTTGGTTTGATACGTAACGCCGCAC
+TGACTCTCATTGCAAAAAACAGGAATAACCATGCAACCGTCCAGAAACTTTGACGATCTCAAATTCTCCT
+CTATTCACCGCCGCATTTTGCTGTGGGGAAGCGGTGGTCCGTTTCTGGATGGTTATGTACTGGTAATGAT
+TGGCGTGGCGCTGGAGCAACTGACGCCGGCGCTGAAACTGGACGCTGACTGGATTGGCTTGCTGGGCGCG
+GGAACGCTCGCCGGGCTGTTCGTTGGCACATCGCTGTTTGGTTATATTTCCGATAAAGTCGGACGGCGCA
+AAATGTTCCTCATTGATATCATCGCCATCGGCGTGATATCGGTGGCGACGATGTTTGTTTCATCCCCCGT
+CGAACTGTTGGTGATGCGGGTACTTATCGGCATTGTCATCGGTGCAGATTATCCCATCGCCACCTCAATG
+ATCACCGAGTTCTCCAGTACCCGTCAGCGGGCGTTTTCCATCAGCTTTATTGCCGCGATGTGGTATGTCG
+GCGCGACCTGTGCCGATCTGGTCGGCTACTGGCTTTATGATGTGGAAGGCGGCTGGCGCTGGATGCTGGG
+TAGCGCGGCGATCCCCTGTTTGTTGATTTTGATTGGTCGATTCGAACTGCCTGAATCTCCCCGCTGGTTA
+TTACGCAAAGGGCGAGTAAAAGAGTGCGAAGAGATGATGATCAAACTGTTTGGCGAACCGGTGGCTTTCG
+ATGAAGAGCAGCCGCAGCAAACCCGTTTTCGCGATCTGTTTAATCGCCGCCATTTTCCTTTTGTTCTGTT
+TGTTGCCGCCATCTGGACCTGCCAGGTGATCCCAATGTTCGCCATTTACACCTTTGGCCCGCAAATCGTT
+GGTTTGTTGGGATTGGGGGTTGGCAAAAACGCGGCACTAGGGAATGTGGTGATTAGCCTGTTCTTTATGC
+TCGGCTGTATTCCGCCGATGCTGTGGTTAAACACTGCCGGACGGCGTCCATTGTTGATTGGCAGCTTTGC
+CATGATGACGCTGGCGCTGGCGGTTTTGGGGCTAATCCCGGATATGGGGATCTGGCTGGTAGTGATGGCC
+TTTGCGGTGTATGCCTTTTTCTCTGGCGGGCCGGGTAATTTGCAGTGGCTCTATCCTAATGAACTCTTCC
+CGACAGATATCCGCGCCTCTGCCGTGGGCGTGATTATGTCCTTAAGTCGTATTGGCACCATTGTTTCGAC
+CTGGGCACTACCGATCTTTATCAATAATTACGGTATCAGTAACACGATGCTAATGGGGGCGGGTATCTCG
+CTGTTTGGCTTGTTGATTTCCGTAGCGTTTGCCCCGGAGACTCGAGGGATGTCACTGGCGCAGACCAGCA
+ATATGACGATCCGCGGGCAGAGAATGGGGTAAATTGTTCAGATTTCTCTCTTTTCTGAATCAATATTATT
+GACTATAAGCCGCGTGAATATATGACTACACTTTGTGGGAAAAC
+>gi|1786230|gb|AE000115|ECAE000115 Escherichia coli , yabF, kefC, folA, apaH, apaG, ksgA, pdxA, surA, imp genes from bases 47163 to 57264 (section 5 of 400) of the complete genome
+GAATCAATATTATTGACTATAAGCCGCGTGAATATATGACTACACTTTGTGGGAAAACAAAGGCGTAATC
+ACGCGGGCTACCTATGATTCTTATAATTTATGCGCATCCGTATCCGCATCATTCCCATGCGAATAAACGG
+ATGCTTGAACAGGCAAGGACGCTGGAAGGCGTCGAAATTCGCTCTCTTTATCAACTCTATCCTGACTTCA
+ATATCGATATTGCCGCCGAGCAGGAGGCGCTGTCTCGCGCCGATCTGATCGTCTGGCAGCATCCGATGCA
+GTGGTACAGCATTCCTCCGCTCCTCAAACTTTGGATCGATAAAGTTTTCTCCCACGGCTGGGCTTACGGT
+CATGGCGGCACGGCGCTGCATGGCAAACATTTGCTGTGGGCGGTGACGACCGGCGGCGGGGAAAGCCATT
+TTGAAATTGGTGCGCATCCGGGCTTTGATGTGCTGTCGCAGCCGCTACAGGCGACGGCAATCTACTGCGG
+GCTGAACTGGCTGCCACCGTTTGCCATGCACTGCACCTTTATTTGTGACGACGAAACCCTCGAAGGGCAG
+GCGCGTCACTATAAGCAACGTCTGCTGGAATGGCAGGAGGCCCATCATGGATAGCCATACGCTGATTCAG
+GCGCTGATTTATCTCGGTTCGGCAGCGCTGATTGTACCCATTGCGGTACGTCTTGGTCTGGGATCGGTAC
+TTGGCTACCTGATCGCCGGCTGCATTATTGGCCCGTGGGGGCTGCGACTGGTGACCGATGCCGAATCTAT
+TCTGCACTTTGCCGAGATTGGGGTGGTGCTGATGCTGTTTATTATCGGCCTCGAACTCGATCCACAAAGG
+CTGTGGAAGCTGCGTGCGGCAGTGTTCGGCTGTGGCGCATTGCAGATGGTGATTTGCGGCGGCCTGCTGG
+GGCTGTTCTGCATGTTACTTGGGCTGCGCTGGCAGGTCGCGGAATTGATCGGCATGACGCTGGCGCTCTC
+CTCTACGGCGATTGCCATGCAGGCGATGAATGAACGCAATCTGATGGTGACGCAAATGGGTCGCAGTGCC
+TTTGCGGTGCTGCTGTTCCAGGATATCGCGGCGATCCCGCTGGTGGCGATGATTCCGCTACTGGCAACGA
+GCAGTGCCTCGACGACGATGGGCGCATTTGCTCTCTCGGCGTTAAAAGTGGCGGGTGCGCTGGTGCTGGT
+GGTATTGCTGGGGCGCTATGTCACGCGTCCGGCGCTGCGTTTTGTAGCCCGCTCTGGCTTGCGGGAAGTG
+TTTAGTGCCGTGGCGTTATTCCTCGTGTTTGGCTTTGGTTTGCTGCTGGAAGAGGTCGGCTTGTCGATGG
+CGATGGGCGCGTTTCTGGCGGGCGTACTGCTGGCAAGCTCGGAATACCGTCATGCGCTGGAGAGCGATAT
+CGAACCATTTAAAGGTTTGCTGTTGGGGCTGTTTTTCATCGGTGTTGGCATGTCGATAGACTTTGGCACG
+CTGCTTGAAAACCCATTGCGCATTGTCATTTTGCTGCTCGGTTTCCTCATCATCAAAATCGCCATGCTGT
+GGCTGATTGCCCGACCGTTGCAAGTGCCAAATAAACAGCGTCGTTGGTTTGCGGTGTTGTTAGGGCAGGG
+CAGTGAGTTTGCCTTTGTGGTATTTGGCGCGGCGCAGATGGCGAATGTGCTGGAGCCGGAGTGGGCGAAA
+TCGCTGACCCTGGCGGTGGCGCTGTCGATGGCAGCAACGCCGATTCTGCTGGTGATCCTCAATCGCCTTG
+AGCAATCTTCTACTGAGGAAGCGCGTGAAGCCGATGAGATCGACGAAGAACAGCCGCGCGTGATTATCGC
+CGGATTCGGTCGTTTTGGGCAGATTACCGGACGTTTACTGCTCTCCAGCGGGGTGAAAATGGTGGTACTC
+GATCACGATCCGGACCATATCGAAACCTTGCGTAAATTTGGTATGAAAGTGTTTTATGGCGATGCCACGC
+GGATGGATTTACTGGAATCTGCCGGAGCGGCGAAAGCGGAAGTGCTGATTAACGCCATCGACGATCCGCA
+AACCAACCTGCAACTGACAGAGATGGTGAAAGAACATTTCCCGCATTTGCAGATTATTGCCCGCGCCCGC
+GATGTCGACCACTACATTCGTTTGCGTCAGGCAGGCGTTGAAAAGCCGGAGCGTGAAACCTTCGAAGGTG
+CGCTGAAAACCGGGCGTCTGGCACTGGAAAGTTTAGGTCTGGGGCCGTATGAAGCGCGAGAACGTGCCGA
+TGTGTTCCGCCGCTTTAATATTCAGATGGTGGAAGAGATGGCAATGGTTGAGAACGACACCAAAGCCCGC
+GCGGCGGTCTATAAACGCACCAGCGCGATGTTAAGTGAGATCATTACCGAGGACCGCGAACATCTGTCAT
+TAATTCAACGACATGGCTGGCAGGGAACCGAAGAAGGTAAACATACCGGCAACATGGCGGATGAACCGGA
+AACGAAACCCTCATCCTAATAAAGAGTGACGTAAATCACACTTTACAGCTAACTGTTTGTTTTTGTTTCA
+TTGTAATGCGGCGAGTCCAGGGAGAGAGCGTGGACTCGCCAGCAGAATATAAAATTTTCCTCAACATCAT
+CCTCGCACCAGTCGACGACGGTTTACGCTTTACGTATAGTGGCGACAATTTTTTTTATCGGGAAATCTCA
+ATGATCAGTCTGATTGCGGCGTTAGCGGTAGATCGCGTTATCGGCATGGAAAACGCCATGCCGTGGAACC
+TGCCTGCCGATCTCGCCTGGTTTAAACGCAACACCTTAAATAAACCCGTGATTATGGGCCGCCATACCTG
+GGAATCAATCGGTCGTCCGTTGCCAGGACGCAAAAATATTATCCTCAGCAGTCAACCGGGTACGGACGAT
+CGCGTAACGTGGGTGAAGTCGGTGGATGAAGCCATCGCGGCGTGTGGTGACGTACCAGAAATCATGGTGA
+TTGGCGGCGGTCGCGTTTATGAACAGTTCTTGCCAAAAGCGCAAAAACTGTATCTGACGCATATCGACGC
+AGAAGTGGAAGGCGACACCCATTTCCCGGATTACGAGCCGGATGACTGGGAATCGGTATTCAGCGAATTC
+CACGATGCTGATGCGCAGAACTCTCACAGCTATTGCTTTGAGATTCTGGAGCGGCGGTAATTTTGTATAG
+AATTTACGGCTAGCGCCGGATGCGACGCCGGTCGCGTCTTATCCGGCCTTCCTATATCAGGCTGTGTTTA
+AGACGCCGCCGCTTCGCCCAAATCCTTATGCCGGTTCGACGGCTGGACAAAATACTGTTTATCTTCCCAG
+CGCAGGCAGGTTAATGTACCACCCCAGCAGCAGCCGGTATCCAGCGCGTATATACCTTCCGGCGTACCTT
+TGCCCTCCAGCGATGCCCAGTGACCAAAGGCGATGCTGTATTCTTCAGCGACAGGGCCAGGAATCGCAAA
+CCACGGTTTCAGTGGGGCAGGGGCCTCTTCCGGCGATTCTTTGCTGTACATATCCAGTTGACCGTTCGGG
+AAGCAAAAACGCATACGGGTAAAAGCGTTGGTGATAAAACGCAGTCTTCCCAGCCCCCGCAATTCCGGTG
+ACCAGTTATTTGGCATATCGCCGTACATGGCATCAAGAAAGAAGGGATAGGAGTCACTCGATAGCACCGC
+TTCTACATCGCGTGCGCACTCTTTGGCGGTCTGCAGATCCCACTGCGGCGTGATCCCTGCGTGGGCCATC
+ACCAGCTTTTTCTCTTCGTCGATTTGCAGCAGAGGCTGGCGCCGCAGCCAGTTAAGCAGCTCGTCGGCAT
+CCGGCGCTTCCAGCAGCGGTGTCAGGCGATCTTTCGGTTTATTGCGGCTGATCCCGGCAAATACCGCCAG
+CAGATGCAGATCGTGATTGCCCAGCACCAGACGTACGCTGTCGCCTAAGGATTTCACATAGCGCAGAACA
+TCCAGCGAACCCGGCCCGCGCGCGACCAGATCGCCCGTCAGCCAGAGGGTATCTTTCCCAGGGGTAAATT
+CTACTTTATGCAGCAATGCGATCAGTTCATCGTAACAACCATGAACGTCGCCAATAAGGTATGTCGCCAT
+ATTCTTTTAATGAATGAGTGTGGGAACGGCGAGTCGGAATACGGGAATGTCGATGCTGAAAGGGACGCCA
+TTTTCATCGATCATTTCGTAGTGACCCTGCATGGTGCCCAGCGGGGTTTCAATGATTGCACCGCTGGTGT
+ACTGGTACTCTTCGCCAGGCGCGATAAGTGGCTGGACGCCAACCACTCCTTCGCCCTGGACTTCGGTTTC
+ACGGCCATTGCCATTGGTGATCAGCCAGTAACGCCCCAACAACTGCACTGGCGCTCGCCCCAGATTGCGT
+ATGGTTACGGTATAAGCAAAAACGTAACGTTCATTATCAGGTGAAGATTGAGCCTCAATGTAGACGCTTT
+GAACCTGAATACACACTCGGGGCGAATTGATCATCGTTAACTCTCCTGCAAAGGCGCGTTCTCCGCCAGA
+TAGTTCGCCATCTGGCAATATTGCGCGACAGAGATATTTTCCGCTCGCATCGCCGGGTCGATCCCCATTC
+CCGTTAACACCTCGACGCTAAACAGGTTGCCGAGGCTGTTACGAATGGTTTTACGACGCTGGTTAAAGGC
+TTCGGTGGTGATGCGGCTCAACACACGAACATCTTTAACCGGGTGAGGCATCGTTGCATGAGGAACCAGG
+CGCACGACGGCGGAATCCACTTTGGGTGGTGGTGTAAAGGCTGACGGCGGTACTTCCAGTACCGGGATCA
+CATTGCAATAGTATTGCGCCATGACGCTTAATCGACCATACGCTTTGCTGTTCGGTCCTGCAACCAGACG
+ATTCACCACCTCTTTTTGCAACATAAAGTGCATGTCGGCAATGGCATCAGTATAGCTAAACAGATGGAAC
+ATCAACGGCGTGGAGATGTTATAAGGCAGGTTGCCGAAAACACGCAGCGGCTGACCCATTTTCTCGGCCA
+GTTCACCAAAGTTAAAGGTCATCGCATCCTGCTGATAAATCGTCAGTTTCGGGCCTAAGAATGGATGCGT
+TTGCAGACGTGCCGCCAGATCGCGGTCAAGTTCGATGACCGTCAGCTGGTCCAGACGTTCGCCGACCGGT
+TCGGTCAATGCCGCCAGACCGGGGCCGATTTCGACCATCGCCTGGCCCTTTTGCGGGTTAATGGCAGACA
+CAATACTGTCGATCACGAACTGATCGTTGAGAAAGTTTTGCCCGAAGCGTTTACGGGCTAAGTGGCCCTG
+GTGGACTCGATTATTCATTGGGTGTTAACAATCATTTTGATGGCGAGATTAAGCGCCGTAATAAAACTGC
+CGACATCGGCTTTGCCACGTCCCGCCAGTTCAAGCGCGGTGCCGTGGTCCACTGATGTGCGAATAAAGGG
+CAGGCCCAGCGTAATGTTCACACCGCGCCCGAAGCCCTGGTATTTTAGCACGGGAAGACCCTGATCGTGG
+TACATCGCCAGCACGGCGTCGGCGTTATCAAGATATTTCGGCTGAAACAGGGTATCGGCAGGCAGCGGCC
+CGTTGAGTTTCATCCCCTGCGCCCGCAGCTCATTGAGCACCGGAATAATGGTGTCTATCTCTTCCGTACC
+CATATGACCGCCTTCGCCCGCGTGCGGATTCAGCCCGCAGACCAGAATGCGCGGTTCGGCAATACCAAAT
+TTGGTCCGCAAATCGTGATGCAAAATAGCAATCACTTCGTGCAAAAGTGCAGGGGTGATAGCGTCTGCGA
+TATCGCGCAGCGGTAAATGCGTCGTTGCCAGCGCCACGCGAAGTTCTTCGGTCGCCAGCATCATCACCAC
+CTTTTTCGCCTGCGAACGCTCTTCGAAAAACTCGGTATGACCGGTAAAAGGAATGCCAGCGTCGTTAATA
+ACGCCTTTATGCACCGGACCTGTGATCAGCGCGGCAAATTCGCCGTTCAGACAACCATCGCACGCTCGCG
+CCAGCGTTTCCACCACATAATGCCCATTTTCAACCGCTAACTGCCCCGCAGTGACAGGTGCACGTAGCGC
+GACAGGAAGTAGCGTTAATGTGCCCGCAGTTTGCGGTTGTGCAGGGGAGTTGGGGGAATAAGGGCGGAGG
+GTGAGCGGCAAACCGAGCATCGCTGCCCGGTTGGTAAGGAGAGTGGCATCGGCACAAACAACCAGTTCGA
+CCGGCCACTCACGCTGTGCAAGCTGGACAACTAAGTCCGGGCCAATCCCGGCGGGCTCGCCGGGAGTGAT
+CACAACACGTTGGGTTTTAACCATTAGTTGCTCAGGATTTTAACGTAGGCGCTGGCACGTTGTTCCTGCA
+TCCAGCTTGCTGCTTCTTCCGAGAACTTACGGTTCATCAGCATGCGGTATGCACGATCTTTCTGCGCAGC
+GTCGGTTTTATCGACATTACGGGTATCCAGCAGTTCGATTAAATGCCAGCCGAATGAAGAGTGAACCGGT
+GCACTCATTTGACCTTTGTTCAGGCGAGTCAGGGCGTCACGGAAGGCCGGATCGAAAATATCTGGTGTAG
+CCCAGCCGAGATCGCCGCCCTGGTTAGCAGAGCCTGGATCCTGAGAGAACTCTTTCGCTGCGGCAGCAAA
+AGTCGTTTTACCACTCTTGATATCAGCAGCAATCTGTTCCAGTTTCACACGGGCCTGTTCGTCAGTCATG
+ATCGGCGACGGTTTCAGCAGAATATGGCGAGCATGAACTTCGGTCACCGAGATATTTTTGCTTTCGCCGC
+GCAGGTCGTTAACTTTCAGAATATGGAAGCCAACGCCGGAACGAATCGGGCCAACAATGTCGCCTTTCTT
+CGCGGTGCTTAATGCCTGGGCGAAGATCCCGGGCAACTCCTGAATACGGCCCCAGCCCATCTGGCCGCCG
+TTCAGCGCCTGCTGGTCGGCAGAATGAGCAATCGCCAGCTTACCGAAATCAGCGCCGTTACGCGCCTGAT
+CGACAATGGCGCGCGCCTGGCTTTCCGCTTCGTTCACCTGATCAGAGGTCGGGTTTTCCGGCAGCGGGAT
+CAGGATGTGGCTCAGGTTCAGCTCAGTGCTGGCGTCGTTTTGGTTACCCACCTGCTGCGCCAGGGATTCG
+ACTTCCTGCGGCAGGATGGTGATGCGACGACGCACCTCGTTGTTACGCACTTCAGAGATAATCATCTCTT
+TGCGGATCTGGTTACGATAGGTGTTGTAGTTCAGTCCATCGTAAGCCAGACGGCTGCGCATCTGATCCAG
+CGTCATGTTGTTCTGTTTCGCGATGTTAGCAATCGCCTGATCCAGCTGCTCATCGGAGATTTTCACTCCC
+ATTTTCTGCCCCATCTGCAGGATGATTTGATCCATGATCAAACGTTCCATGATTTGGTGGCGCAGCGTCG
+CGTCATCAGGAAGTTGCTGCCTTGCCTGAGCAGCGTTCAGTTTTACCGACTGCATTAATCCATCAACGTC
+GCTTTCCAGCACGACGCCGTTATTGACGACGGCTGCGACTTTATCGACTACCTGGGGGGCAGCGAAACTG
+GTATTCGCGATCATGGCGATACCGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAA
+CCGCACTGCGGATTACGTGGTAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCA
+GCATCTCTTGCGTACCCAGACCGTAGTTGGAGCTCAGGCCGCGAAGTTCGATGTTAAAGCCGATTGCGTT
+GTCATATACCGCATGTTGTTTATCGTTATCCCAACCGTTCAGCTTCCGCTCGTAACCGACGCGAATTGCA
+TAGCAGCAGGAGCTGTATTGCACACCTAACATAGAGTCGGCTTGCTTGTTAGCATTGGTGTCGTAGTAGT
+AGGCCCCAACAATGGACCAACGATCGGCAATTGGCCAGCTGGCGACAGCACCTACCTGCGAAATACCATT
+CTTATATTGCTCAGCAGTGGAATAGTACTTAGGCAGCGTAGCCTGAATATATTCCGGGCTGGCGTAACGG
+TAATTCAGCTGTACCAGACGGTCTTCATCCCGACGGTATTCAATGCTGGAGTTACTGGTCGCTACGTTAT
+CCAGACGTGTATCGTACTGAATCCCGCCACGCAATCCCCAACGCTCGGAGATACGCCAGTAAGTATCGCC
+TGCCCACACCAGTGAACCCGTTTTGTCGTCATTCTCCCATGTTATGTTGTCATCGCCAGTGCGAGACTCC
+GTGAAATAGTAGATTTGACCAACGGAAATATTAAAACGTTCAACGGCAGCATCATCATATATGCGAGATG
+TGACACCGGTCGTCACCTGGTTAGCGGAGGCAATACGGTCAAGACCGCCGTAAGTCCGGTCCCGGAACAG
+GCCAGAGTAGTCAGATTGCAGCAGAGACGAGTCGTAGTTATAGATGTCGCTCTGATCGCGATACGGCACG
+TACAAATACTGCGCGCGCGGTTCCAGCGTTTGGGTATAACCCGGAGCCAGCATTTCCATATCGCGTTCAA
+AGACCATTTTGCCGTCAACTTTGAATTGCGGCATTACGCGGTTAACGGATTCGTCCAGCTTGGTCGTGTT
+TCTGGAGTTATACCAGTCAAGATTGGTTTGCTGATAATGGGTTGCCAGCAACTTCGCTTCGGTATTGATG
+CTGCCCCAGTTATTAGAGAGCGGCAAATTGATGGTCGGTTCCAGGTGAACACGGGTTGCTTCAGGCATGT
+CGTCTCTGGTGTTAACAAAGTGCACTGCCTGGCCGTAAATACGCGTATCAAACGGACCAACATCATTCTG
+GTAGTAATTAACGTCTAACTGCGGCTCTGCCGAGTAGCTACTGGTGTTCTGTTCGCTGAAAACCTGGAAC
+TGCTTGGTTGAAACGGTGGCATTGAAGTTTTGCACCGCATAGCCAACGCTGAATTTTTGCGTTGCGTAGC
+CGTCAGTACTGGAACCGTACTTGTTATCGAAATCATTGAAGTAGCTAGGATCGCTGACCTTGGTGTAGTC
+GACGTTGAAACGCCACACCTGATCCATGACCCCGGAGTGGTTCCAGTAGAATAACCAACGACGTGAACTG
+TCATCGTTCGGGTGTTCATCTTCATAGACTTTATCTGAAGGCAGATAGTCCAGTTCCATCAAGCCAGCGC
+CCGCCTGGGAGAGGTAGCGGAATTCGTTCTCCCACATGATGTTGCCACGACGATGCATATAATGCGGCGT
+GATGGTGGCATCCATATTTGGCGCGATGTTCCAGTAATATGGCAGGTAGAACTCAAAGTAGTTGGTGGTG
+GTGTACTTGGCGTTCGGGATCAAGAAACCAGAGCGACGTTTGTCACCCACCGGCAACTGCAAATAGGGGC
+TATAAAAGATCGGTACCGGACCCACCTTAAAGCGGGCGTTCCAGATCTCCGCAACTTGTTCTTCGCGGTC
+ATGAATAATTTCGCTACCTACCACGCTCCAGGTGTCAGAACCCGGCAGACAGGAGGTAAAGCTACCGTTA
+TCCAGAATGGTATAGCGGTTTTCGCCACGTTGTTTCATCAGGTCCGCTTTACCGCGACCCTGGCGACCCA
+CCATCTGGTAATCACCTTCCCAGACGTTGGTATCTTTGGTGTTCAGATTCGCCCAGCCTTTCGGCCCTTT
+GAGGATCACCTGGTTATCGTCGTAATGGACATTACCGAGCGCATCAACGGTACGTACCGGCTCCGGTTGT
+CCTGGTGCCTCTTTTTGATGGAGCTGCACTTCGTCGGCCTGCAGACGGCTGTTACCCTGCATGATATCCA
+CGCTGCCAGTAAACACGGCGTCATCCGGGTAGTCCCCTTTCGCGTGGTCAGCATTGATAGTCACGGGTAA
+GTCATTGGTATCGCCCTGTACCAGAGGACGGTCATAGCTTGGCACGCCCAACATGCACTGTGAGGCGAGG
+TCGGCTGCCAGTCCCTGTTGACTATAAAGGGCGGTGGCAATCATGGTGGCCAGGAGAGTGGGGATACGTT
+TTTTCATACGTTGATTTTATTGTTCCATCATCGGTAACGTTGCGCGTGACAAACGGTCAGAGACTAACGT
+ACTCGTCATCTCTACGCTAGTGTTAATCCTGTCCGAATAGCGTCAGTGGTGTTAGGCACGGCATTGAATG
+ACAGGTATGATAATGCAAATTA
+>gi|1786240|gb|AE000116|ECAE000116 Escherichia coli , yabH, yabP, yabQ, yabO, hepA, polB, araD, araA, araB genes from bases 57207 to 70245 (section 6 of 400) of the complete genome
+GAATAGCGTCAGTGGTGTTAGGCACGGCATTGAATGACAGGTATGATAATGCAAATTATAGGCGATGTCC
+CACAATTGACCGCAGCCGGAAAACGGTAAAAGCACCTTTATATTGTGGGAGATAGCCCTGATATCCGTGT
+GTCGATTTGGGGAATATATGCAGTATTGGGGAAAAATCATTGGCGTGGCCGTGGCCTTACTGATGGGCGG
+CGGCTTTTGGGGCGTAGTGTTAGGCCTGTTAATTGGCCATATGTTTGATAAAGCCCGTAGCCGTAAAATG
+GCGTGGTTCGCCAACCAGCGTGAGCGTCAGGCGCTGTTTTTTGCCACCACTTTTGAAGTGATGGGGCATT
+TAACCAAATCCAAAGGTCGCGTCACGGAGGCTGATATTCATATCGCCAGCCAGTTGATGGACCGAATGAA
+TCTTCATGGCGCTTCCCGTACTGCGGCGCAAAATGCGTTCCGGGTGGGAAAATCAGACAATTACCCGCTG
+CGCGAAAAGATGCGCCAGTTTCGCAGTGTCTGCTTTGGTCGTTTTGACTTAATTCGTATGTTTCTGGAGA
+TCCAGATTCAGGCGGCGTTTGCTGATGGTTCACTGCACCCGAATGAACGGGCGGTGCTGTATGTCATTGC
+AGAAGAATTAGGGATCTCCCGCGCTCAGTTTGACCAGTTTTTGCGCATGATGCAGGGCGGTGCACAGTTT
+GGCGGCGGTTATCAGCAGCAAACTGGCGGTGGTAACTGGCAGCAAGCGCAGCGTGGCCCAACGCTGGAAG
+ATGCCTGTAATGTGCTGGGCGTGAAGCCGACGGATGATGCGACCACCATCAAACGTGCCTACCGTAAGCT
+GATGAGTGAACACCATCCCGATAAGCTGGTGGCGAAAGGTTTGCCGCCTGAGATGATGGAGATGGCGAAG
+CAGAAAGCGCAGGAAATTCAGCAGGCATATGAGCTGATAAAGCAGCAGAAAGGGTTTAAATGACCCTGTA
+AATGATGCTGAGTAACTGCCCACGATTAAAGGTGGCCGCCCTGGCGGTCACTTCTTTGAGAAAAGGCGTT
+TACTCAGAATGGTGGACAGGCTCAATGCACGGTTTACGGGAGGGGTTCTGTAGGTTTTATCGCGTTGACC
+CTGCTTAAGGTTGAGAGCTTTACGACGAGCGGAATTATATTTTTACGTCTTAAAAATAAAAAACACATAC
+CTGAATGAGCGATTTTTGAAAGTATATTTATTCAGAACGCGCATCATGAGTTTTTAACTCAATGCGAGGC
+TATTACCATGAAAGTATCAGTTCCAGGCATGCCGGTTACACTTTTAAATATGAGCAAGAACGATATTTAT
+AAGATGGTGAGCGGGGACAAGATGGACGTGAAGATGAATATCTTTCAACGCTTGTGGGAGACGTTACGCC
+ATCTGTTCTGGTCAGATAAACAGACTGAGGCTTATAAACTTCTGTTCAATTTCGTGAATAACCAGACTGG
+CAACATCAACGCCTCAGAATACTTTACTGGGGCTATCAACGAGAATGAGAGAGAAAAGTTTATCAATAGC
+CTGGAATTATTCAATAAACTTAAAACATGCGCAAAAAATCCGGATGAGTTGGTCGCAAAGGGCAATATGC
+GCTGGGTCGCCCAGACCTTCGGGGATATCGAGTTAAGTGTCACTTTTTTCATTGAAAAGAATAAGATATG
+TACTCAGACGTTGCAGCTGCATAAGGGCCAAGGTAACTTGGGCGTTGATCTTAGAAAGGCTTACCTTCCC
+GGCGTTGACATGAGGGATTGTTACCTTGGTAAAAAAACAATGAAAGGTAGCAATGATATCCTTTATGAGA
+GACCTGGGTGGAATGCTAACCTGGGCGTGCTACCCCGGACGGTGCTACCCCGGACGGTGCTAACCCGGAC
+GGTGCTAACCTGGACGGTGCTACCGTGAACGGTGCTACCTCCTTATATGATGAGGTAATTATTATTAATA
+AAATCCCCCCCAAAAAAATTGATACTAAAGGAGTTGCTACTGAAGAAGTTGCTACTAAAAAAGTACTGCT
+GAACAAATTACTGACAACGCAATTATTGAATGAGCCAGAATAAGCTAAGGTTGAAGGGGCTGGAACGCCC
+CTTCAACCTTAGCAGTAGCGTGGGATGATTTCACAATTAGAAAGACCTGCATGATGAGCTAGAGAAGAGG
+CTAGTGACGCAAGGCGTCGTGCAGGACACGGATCACCGAGATGGGCATCGCCAACCAGACTGCTAATTAG
+CCCATGAATAACAATCAGAAAGGACCATAACAGACCCGTTAAAATGAAATATAAGAGACGGTCAACGGGT
+GAAGAAAAAGTTCAAAAATTCGCTGTGGAGCAGGAAGGGAATTACCGAATGGAAAGCGTAGCCACACGCA
+ACAACTGAAAGCAGTTTGGCAGAAACAAAAAATCCCCGGACTCGGGGATTTATGTACAAGAGGCAGCCCT
+TAGGATGAGGGTATAAACGTACAGGAAAGGTTAAAAATCCGCTGGCGCTTTAAACGTCATACTATTGCCA
+TACGCCGGATGGGTAATCGTCAACATCTCTGCATGTAGCAACAAACGTGGTGCCATCGCTCTCGCTTCTG
+GTGATGCATAAAAACGATCGCCGAGAATCGGATGACCCAGCGCCAGCATATGCACACGCAATTGATGCGA
+ACGCCCGGTAATCGGTTTTAACACCACTCTTGCCGTGTTATCCGCCGCATACTCCACCACTTCATATTCC
+GTCTGCGCAGGTTTACCCGTTTCGTAACAGACTTTCTGTTTCGGGCGGTTTGGCCAGTCGCAAATCAGCG
+GCAGATCCACCAGACCTTCTGCGGGGGATGGATGCCCCCAGACGCGGGCCACATACTGCTTTTTCGGCTC
+GCGCTCGCGGAACTGGCGTTTTAACTCCCGCTCCGCGGCTTTGGTCAGCGCCACTACAATCACGCCGCTG
+GTAGCCATATCCAGACGATGCACCGATTCTGCCTGCGGATAATCACGCTGAATGCGCGTCATCACGCTGT
+CTTTGTGCTCTTCCAGACGACCCGGCACTGACAACAAACCGCTCGGCTTGTTGACCACCATAATATGGTC
+ATCCTGATACAGGATAACCAACCAGGGTTCCTGCGGTGGATTGTAGTTTTCCATCCCCATTTTCGGCTCC
+GTTACTGATGCGTTACAACGATCAAACGCAGGGCATCCAGACGCCAACCTGCCTGATCCAGGCTTTCCAT
+TACCTGCTGACGGTTGCTCTCAATGGCGGTCAGTTCGTCGTCACGAATGTTCGGGTTCACTGCACGCAGA
+GCTTCCAGACGAGACAGCTCGGCAGACAGTTTTTCGTCGGCTTCGTTACGCGCTGCATCAATCAATGCAC
+GGGCAGATTTCTCGATCTGCGCTTCACCCAGTTGAAGGATAGCGTGAACATCCTGCTGCACGGCGTTAAC
+CAGTTTGCTGCCGGTGTGACGGTTAACCGCGTTAAGCTGGCGGTTAAAGGTTTCAAACTCTACCTGCGCC
+GCCAGGTTGTTGCCGTTTTTATCCAGCAGCATACGTACCGGCGTCGGTGGCAGGAAGCGGTTGAGCTGCA
+ACTGCTTCGGAGCCTGGGCTTCAACCACATAAATCAGTTCCACCAACAGCGTACCTACCGGCAACGCTTT
+GTTTTTTAACAGTGAAATCGTGCTGCTACCGGTATCGCCAGAAAGGATCAGATCCAGACCGTTGCGGATC
+AGCGGATGCTCCCAGGTAATAAACTGTGCATCTTCACGCGCCAGCGCCACTTCACGATCAAAGGTGATGG
+TGATGCCATCTTCCGACAGGCCAGGGAAGTCCGGCACCAGCATATGATCGGACGGCGTCAGCACGATCAT
+GTTGTCGCCGCGATCGTCCTGATTGATACCGATAATATCGAACAGGTTCATGGCGAAGGCGATCAGGTTG
+GTATCGTCATCCTGCTCTTCAATGCTTTCTGCCAGTGCCTGGGCTTTTTCGCCACCGTTGGAGTGGATTT
+CCAGCAGGCGGTCACGACCCTGTTCCAGCTGTGCTTTCAGCGCTTCATGTTGCTCGCGGCAGTTTTTGAT
+CAGATCGTCAAAGCCTTCGGTTTGATCCGGTGAAGCCAGATAGTTAATCAGATCGTTGTATACGCTATCG
+TAAATAGTGCGTCCGGTCGGGCAGGTGTGCTCAAATGCATCCAGACCTTCGTGATACCAGCGCACCAGCA
+CCGACTGAGCGGTTTTCTCCAGATAAGGCACATGGATCTGAATATCGTGCGCCTGGCCGATACGATCCAG
+ACGACCAATACGCTGCTCCAGTAGATCCGGGTTGAATGGCAGGTCAAACATCACCATGTGGCTGGCGAAC
+TGGAAGTTACGTCCTTCAGAACCGATTTCTGAGCACAGCAGTACCTGTGCGCCGGTGTCTTCTTCGGCAA
+ACCAGGCGGCAGCGCGGTCACGTTCGATAATCGACATACCTTCGTGGAACACCGCAGCGCGAATACCTTC
+ACGTTCGCGCAGTACCTGCTCCAGTTGCAGCGCAGTGGCAGCTTTGGCGCAGATCACCAGCACTTTCTGA
+GAGCGATGGCTGGTCAGGTAGCCCATCAGCCACTCAACGCGCGGATCGAAGTTCCACCAGGTGGCGTTAT
+CACCTTCAAATTCCTGATAAATACGCTCCGGGTAGAGCATATCGCGAGCACGATCTTCCGCACTTTTACG
+TGCGCCCATAATGCCGGAGACTTTAATAGCCGTCTGATACTGCGTCGGTAGCGGCAGCTTAATGGTGTGC
+AGCTCGCGTTTCGGGAATCCTTTCACACCGTTACGCGTGTTACGGAACAGCACGCGGCTGGTGCCGTGGC
+GATCCATCAGCATCGAAACCAGCTCCTGACGGGCGCTCTGGGCATCTTCGCTGTCGCTGTTTGCTGCCTG
+CAACAGCGGCTCGATATCCTGCTCGCCGATCATCTCGCCGAGCATGTTCAGTTCGTCATTGCTCAGTTTG
+TTACCTGCCAGCAGCATGGCAACGGCGTCCGCAACCGGACGATAATTTTTCTGCTCTTCAACGAACTGCG
+CAAAATCGTGGAAACGGTTCGGGTCCAGCAGACGCAGACGGGCGAAGTGGCTTTCCATCCCCAGCTGTTC
+CGGGGTCGCGGTCAGCAGCAGAACGCCCGGCACGTGCTCTGCCAGTTGTTCAATGGCCTGATATTCACGG
+CTTGGCGCATCTTCGCTCCACACCAGGTGATGCGCTTCATCGACCACCAGCAGGTCCCATTCGGCTTCAC
+AGAGATGTTCCAGGCGCTGTTTGCTACGACGGGCAAAATCCAGCGAGCAAATCACCAGCTGTTCGGTGTC
+AAACGGGTTGTAAGCATCGTGCTGAGCTTCGGCATAACGCTCATCATCAAATAGCGCAAAGCGCAGGTTG
+AAACGGCGCAGCATTTCTACCAGCCACTGATGCTGTAAGGTTTCCGGGACGATAATTAGCACACGTTCAG
+CAGCGCCAGAGAGCAGTTGCTGATGCAGGATCATCCCGGCTTCAATGGTTTTCCCTAAACCCACTTCGTC
+AGCCAGCAGGACGCGCGGCGCGTGGCGGCGACCAACATCATGAGCGATGTTGAGCTGATGCGGGATCAGG
+CTGGTACGCTGACCGCGCAGGCCGCTGTACGGCATACGGAACTGTTCGCTGGAATATTTACGCGCGCGAT
+AACGCAGCGCAAAGCGGTCCATACGGTCAATCTGCCCGGCAAACAGACGGTCCTGCGGTTTGCTGAACAC
+CAGTTTGCTATCAAGGAAAACTTCACGCAGGGCTACGCCGGACTCTTCAGTATCCAGGCGAGTACCGATA
+TAGGTCAGCAAGCCATTTTCTTCTTTTACTTCTTCGACTTGCATCTGCCAGCCGTCATGGCTGGTAATGG
+TATCACCAGGGTTGAACATCACGCGGGTCACGGGGGAATCACTGCGTGCGTACAGACGGTTTTCACCAGT
+AGATGGGAAAAGTAAAGTGACAGTTCGCGCATCCACCGCGACAACGGTTCCAAGTCCCAATTCGCTTTCT
+GTATCGCTGATCCAGCGTTGACCAAGTGTAAAAGGCATATGTGTTCGGCTCTATATCTTTAATTGCAGGC
+AATAACCACCCGCTACCGTGCTTATGAGGTAGTGGTGTTATTCAGGTCCAGGAATGGAAAGGGCGCTATG
+GTACTGGATGGCAAAGCATTCGTCACGCATCAAAATGGTATCTGGCGAACTCTTTTTTTTGCTCAAAATA
+GCCCAAGTTGCCCGGTCATAAGTGTAGCAAAATTATCCTCAATAAAAGGGAGTATTCCCTCCGCCACGGG
+TTGTAGCTGGCGGGTCAGATAGTGTTCGTAATCCAGTGGTGAACGTTGGTAGTCCAGCGGCTCCGGGCCG
+TTGGTGGTCCATACGTACTTAATGGTGCCGCGATTCTGATATTGCAAGGGGCGACCACGCTTTTGGTTTT
+CTTCATCGGCAAGGCGAGCGGCGCGTACATGAGGCGGCACATTACGCTGATACTCGCTCAGCGGACGGCG
+AAGGCGTTTACGGTAAACCAGTCGCGCATCCAGTTCACCCGCCATCAGTTTGTCGATGGTTTCGCGTACA
+TATTCCTGATATGGCTCGTTGCGGAAGATGCGCAGGTATAGCTCCTGCTGAAACTGCTGGGCCAGCGGCG
+TCCAGTCGGTGCGCACGGTTTCCAGCCCTTTAAACACCATCCGCTGCTTGTCGCCCTCCTGAATCAGTCC
+GGCATAACGCTTTTTACTGCCGGTATCGGCTCCGCGAATGGTTGGCATCAGAAAACGGCAGAAATGGGTT
+TCATACTCCAGTTCTAATGCGCTGGTCAGCCGTTGTTTTTGCAGCGTTTCCGCCCACCAGGCGTTAACGT
+GCTGCACCAGTGCACGACCGATTTTCGCCGCTTCTTCTTCCGAATGTGCGCCTTTCAGCCAGACAAACGT
+TGAGTCGGTATCGCCGTAGATAACGTCGTAGCCCTGTGCTTCAATCAACGCTTTGGTTTGCCGCATGATC
+TGATGACCACGCATGGTGATCGACGATGCCAGCCGCGGATCGAAGAAGCGGCAGGCGGTGGTGCCGAGCA
+CGCCATAAAAGGCATTCATGATGATTTTCAGCGCCTGCGACAGCGGTTTGTTACCCTGGCGTTTGGCTTC
+ATCGCGCCCGTGCCAGATGTTAGTCACAATCTCCGGCAGGCAATGTTTTTCTCGCGAGAACCAGGCATCG
+AGAAAACCTTCGGTACTGTGCTCTGGATCAGGCTGCGCCATGCCTTCCACCAGCCCGACGGGATCAATCA
+GAAAGGTGCGGATGATCGACGGGTACAGGCTTTTATAGTCCAGCACCAGCACTGAATCATAAAGCCCTGG
+CCGTGAATCCATCACGTAGCCGCCAGGGCTGGCGTGCGGCGGCACTTCGCCGAGATTAGGCGCGACATAA
+CCAGCGCGATGCATTCGCGGAAAATAGAGATGACCAAATGCCGCCACCGAACCGCCGTGTCGGTCCACCG
+GCAGGCCGTTCACCGTTGCCCGTTCGAGTAAAAATGGCATGATTTCAGTTTTGTGGAAGATCTGCGTCAC
+CAGCTCGCAATCTTTCAGGTTATAAGTTGCCAGCGCAGGTTTATCTTCGGCGAAACGGCGGTCAATTTCG
+TCCATTCGATCCCACGGGTTATCGATAGATTTTCCTTCGCCTAATAGCTCCTGAGCGACAGTTTCCAGCG
+AGAATGAAGAGAAATTCCAGAACGCGGATTTCAGCGCCTCGATACCGTCGATAATTAGCCGACCTTTAGC
+CTGGGCAAAAAAGACGCCGTTTTTAAAGCCGTGCTCGCGCCACTCCAGCTCGCTATTATCGCGCCCAAGA
+CGCAGCGGAAGACGGTAACGCTCGGCATGTTTTTGCAGCATTCGCAGATCGAACTGCACCACGTTCCAAC
+CGATGATCACATCAGGATCGTAGTTGGCAAACCAGGCGTTGAGTTTTTCCAGCAACTGCGGGCGGCTGGC
+GACGTATTCCAGTTCGAAATCAAGCGAGGAGGCGTCGCCATTCTCCGGCCCCAGCATATAAACGATGCGC
+TGCCCGCAGCCTTCCAGGCCGATGCAGTACAGCTCACCGTGGCGGGTGGTTTCAATATCTATAGAAACCC
+ACTTGAGCGGCGGACGATAGTCGGGATGCGGTTTCAGACGGGCATTAACGATAGTGCCATTGTGCATATC
+ACCCTCGACCCACACCGGTGAGGTGATAAACCGCTCCATCAGATAGCGTTCTGGCGGACGCACATCGGCC
+TCGTAGACGGTAACGCCACCTTCACGCAGGCGCTTTTCGTAATTCATCAATTGGCGATGGGCGCGACAGT
+AAAGGCCATACACCGGCTGGCGGTGAAAATCCTTTAACGCCAGCGGTGTCAGGCGAAAGCCTTGTTCACC
+CTGCAAAATATGCTGAGCGCGGGGAACCTGATCGGCGGGAATAAACGCCACGGACTCTTGCGGTGCAAGC
+GTAACCTGCAACGGCCCGTTGTCCGTCGCCAGCCAGAAGGAGACTTCTGTCCCTTGCGGGGTGTCCCGCC
+AGTGTCGGGTTAAGATAAAACCTGCCTGCGCCACGCTGAAAATCCATCAAAAAACCAGGCTTGAGTATAG
+CCTGGTTTCGTTTGATTGGCTGTGGTTTTATACAGTCATTACTGCCCGTAATATGCCTTCGCGCCATGCT
+TACGCAGATAGTGTTTATCCAGCAGCGTTTGCTGCATATCCGGTAACTGCGGCGCTAACTGACGGCAGAA
+TATCCCCATATAAGCGACCTCTTCCAGCACGATGGCGTTATGCACCGCATCTTCGGCATTTTTGCCCCAT
+GCAAACGGGCCGTGGGAATGGACCAGAACGCCGGGCATTTGCGCTGCATCGATACCCTGTTTTTCAAAGG
+TTTCTACGATGACGTTACCGGTTTCCCACTCATATTCGCCGTTGATTTCTGCGTCGGTCATTTTGCGGGT
+GCAGGGAATGGTGCCGTAGAAATAGTCGGCGTGGGTGGTGCCGGTTGCTGGAATCGACTGACCCGCCTGC
+GCCCAGATGGTGGCGTGGCGCGAGTGCGTATGCACAATGCCGCCAATGGAGGGGAATGCCTGATAGAGCA
+GCCGGTGAGTTGGCGTGTCGGAGGAGGGCTTTTTCGTACCTTCAACCACTTCACCGGTTTCGATGCTAAC
+CACGACCATATCGTCAGCGGTCATGACGCTGTAATCGACGCCGGAAGGTTTGATCACAAAGACGCCGCGC
+TCGCGATCAACGGCGCTGACGTTGCCCCATGTGAGCGTGACCAGGTTGTGTTTTGGCAGCGCCAGGTTGG
+CTTCTAATACCTGGCGTTTGAGATCTTCTAACATGTTGACTCCTTCGTGCCGGATGCGCTTTGCTTATCC
+GGCCTACAAAATCGCAGCGTGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGGCGTTGAATGCCGGAT
+GCGCTTTGCTTATCCGGCCTACAAAATCGCAGCGCGTAGGCCTGATAAGACGCGCCAGCGTCGCATCAGG
+CGTTGAATGCCGGATGCGCTTTGCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCAGATAAGACGCGT
+CAGCGTCGCATCAGGCGTTACATACCGGATGCGGCTACTTAGCGACGAAACCCGTAATACACTTCGTTCC
+AGCGCAGCGCGTCTTTAAACGCTGGCAGGCGTGTGTCGTTATCAATCACCGTGATTTCAATGTCGTGCAT
+CTCGGCGAATTGGCGCATATCGTTGAGGTTCAGTGCATGGCTGAAGACGGTATGGTGCGCGCCACCAGCG
+AGGATCCACGCTTCGGAAGCAGTTGGCAGATCCGGTTGCGCTTTCCACAGCGCATTCGCCACCGGCAGTT
+TCGGCAGGGAGTGCGGTGTTTTCACCGTGTCGATGCAGTTAACCAGTAGACGGTAACGATCGCCGAGATC
+AATCAAGCTGGCGACAATCGCTGGGCCGGTTTGGGTATTGAAGATCAGGCGGGCAGGATCGTCCTTACCA
+CCAATACCGAGATGCTGAACGTCGAGGATCGGTTTCTCTTCTGCGGCGATCGACGGGCAGACTTCCAGCA
+TATGGGAGCCGAGCACCAGGTCATTACCTTTCTCGAAGTGATAGGTGTAGTCCTCCATAAAGGAGGTGCC
+GCCCTGCAGACCGGTTGACATCACCTTCATGATGCGAAGCAGGGCGGCAGTTTTCCAGTCGCCTTCGCCC
+GCAAAGCCGTAACCCTGCTGCATCAGACGCTGTACGGCCAGACCAGGAAGCTGTTTCAGACCGTGCAAAT
+CTTCAAAGGTGGTGGTGAACGCGTGGAAGCCACCTTGTTCCAGGAAACGCTTCATCCCCAGCTCAATACG
+CGCCGCTTCCAGCACGTTCTGTCGTTTTTTGCCGTGGATTTGTGTGGCAGGCGTCATGGTGTAGCAGCTT
+TCGTACTCATCGACCAGCGCGTTAACATCGCCGTCGCTGATGGAGTTCACCACCTGCACCAGATCGCCAA
+CCGCCCAGGTATTGACGGAGAAACCGAACTTGATCTGTGCGGCAACTTTATCGCCATCGGTGACCGCCAC
+TTCACGCATGTTATCGCCAAATCGGCAGACTTTCAGATGACGGGTATCCTGTTTAGAGACCGCCTGACGC
+ATCCAGGAGCCGATACGCTCATGGGCTTGTTTATCCTGCCAGTGACCGGTAACCACGGCATGTTGCTGAC
+GCATACGCGCGCCAATGAAGCCGAACTCGCGACCGCCATGTGCAGTCTGGTTCAGGTTCATAAAGTCCAT
+ATCGATACTGTCCCACGGCAGCGCCGCGTTGAACTGGGTGTGGAATTGCAGCAACGGTTTGTTGAGCATG
+GTCAGGCCGTTGATCCACATTTTGGCCGGGGAGAAGGTGTGCAGCCACACCACCAGACCAGCGCAACGAT
+CGTCGTAATTCGCGTCGCGGCAAATAGCGGTGATTTCATCCGGCGTGGTGCCCAGCGGTTTCAACACCAG
+TTTGCAGGGCAGTTTCGCTTCCGTATTCAGCGCATTAACGACGTGCTCGGCATGTTGGGTGACCTGACGC
+AGGGTTTCCGGGCCATACAGATGCTGGCTGCCAATGACAAACCACACTTCATAATTATCAAAAATCGTCA
+TTATCGTGTCCTTATAGAGTCGCAACGGCCTGGGCAGCCTGTGCCGGGGCGGAAGTTGGAAGATAGTGTT
+GTTCGGCGCTCATCGCCCATTGCTGATAGCGGCGATAAAGCTGTTCAAAGCGTTGTGCCTGCTCGCTGCA
+CGGTTGCAGGGTTTTCTCTACCGCACTGGCCATTTTTTGCTGAGCTGATGGGATGTCTGCGTGCACTTTC
+GCGGCGACGGCAGCAAAAATCGCCGCACCGAGCGCACAGCACTGGTCAGAGGCAACAATTTGCAGCGGGC
+GATTCAGCACGTCGCAGCAGGCCTGCATAATGACCTGGTTTTTCCGCGCGATGCCGCCCAGTGCCATCAC
+GTTATTAACGGCGATCCCCTGATCGGTAAAGCACTCCATGATTGCGCGTGCGCCAAAGGCGGTGGCAGCA
+ATCAAACCGCCGAACAGCAGCGGAGCGTCGGTAGCGAGGTTAAGATCGGTAATCACCCCTTTCAGGCGTT
+GGTTAGCGTTCGGTGTGCGGCGGCCGTTAAACCAGTCGAGCACCACCGGCAGGTGATCCAGAGACGGATT
+TTTGGCCCATGCTTCGGTCAGCGCCGGAAGCAGTTGTTTCTGGCTGGCGTTGATTTGCGTTTTCAGTTCC
+GGATGCTGGGCGGCAAGCTGTTCCAGCGGCCAGCCGAGTACGCGACCAAACCAGGCGTAGATATCACCAA
+ACGCCGATTGGCCTGCTTCCAGACCGATAAATCCAGGCACCACGCTGCCATCAACCTGACCGCAAATACC
+TTTAACTGCCCGCTCGCCAACGCTCTGTTTGTCGGCAATCAGAATGTCGCAGGTGGAAGTACCGATAACT
+TTTACCAGTGCGTTAGGCTGTGCGCCTGCGCCAACTGCGCCCATATGGCAGTCAAACGCGCCGCCGGAAA
+TCACCACGCTTTCAGGCAGGCCGAGACGCTGCGCCCATTCCGGGCATAAGGTGCCCACCGGAATATCGGC
+AGTCCAAGTGTCAGTGAACAGCGGGGAAGGCAAATGGCGATTGAGGATCGGGTCCAGCTCATCAAAGAAA
+CTGGCTGGCGGCAGGCCGCCCCAGCTTTCGTGCCACAGAGATTTATGCCCGGCGCTGCAACGTCCGCGAC
+GAATATCCTGCGGGCGGGTGGTACCGGAAAGCAGAGCTGGCACCCAGTCGCACAGCTCAATCCACGATGC
+GGCAGATTGCGCCACGGCGCTGTCCTGGCGAGTCACATGCAGGATTTTTGCCCAGAACCATTCGCTGGAA
+TAAATACCACCAATGTAGCGGGAGTAGTCAACGTTGCCCGGCGCGTGGCACAAACGGGTAATCTCTTCCG
+CTTCTTCAACCGCAGTGTGGTCTTTCCACAATACGAACATCGCGTTCGGGTTTTCGGCAAACTCCGGGCG
+CAGCGCCAGCACGTTTCCGTCGGCATCAATCGGTGCGGGCGTCGAGCCGGTACTGTCAACGCCAATCCCG
+ACCACAGCTGCGCGCTGTTCGACGCTAAGCTCTGCAAGCACGGTTTTCAGTGCCGCTTCCATTGACTCAA
+TGTAGTCACGCGGATGATGACGGAACTGGTTATTCGGGGCATCACAAAATTGCCCTTTCTGCCAACGGGG
+ATACCACTCTACGCTGGTGGCGATCTCTTCACCGGTAGCGCAGTCCACCGCCAAAGCTCGCACAGAATCA
+CTGCCAAAATCGAGGCCAATTGCAATCGCCATCGTTTCACTCCATCCAAAAAAACGGGTATGGAGAAACA
+GTAGAGAGTTGCGATAAAAAGCGTCAGGTAGGATCCGCTAATCTTATGGATAAAAATGCTATGGCATAGC
+AAAGTGTGACGCCGTGCAAATAATCAATGTGGACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGT
+TTTTGTCATGGCTTTGGTC
+>gi|1786250|gb|AE000117|ECAE000117 Escherichia coli , araC, yabI, yabJ, yabK, tbpA, yabN, yabM, leuD, leuC, leuB, leuA genes from bases 70188 to 83603 (section 7 of 400) of the complete genome
+GACTTTTCTGCCGTGATTATAGACACTTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTAC
+AGAATGCTTTTAATAAGCGGGGTTACCGGTTGGGTTAGCGAGAAGAGCCAGTAAAAGACGCAGTGACGGC
+AATGTCTGATGCAATATGGACAATTGGTTTCTTCTCTGAATGGTGGGAGTATGAAAAGTATGGCTGAAGC
+GCAAAATGATCCCCTGCTGCCGGGATACTCGTTTAACGCCCATCTGGTGGCGGGTTTAACGCCGATTGAG
+GCCAACGGTTATCTCGATTTTTTTATCGACCGACCGCTGGGAATGAAAGGTTATATTCTCAATCTCACCA
+TTCGCGGTCAGGGGGTGGTGAAAAATCAGGGACGAGAATTTGTCTGCCGACCGGGTGATATTTTGCTGTT
+CCCGCCAGGAGAGATTCATCACTACGGTCGTCATCCGGAGGCTCGCGAATGGTATCACCAGTGGGTTTAC
+TTTCGTCCGCGCGCCTACTGGCATGAATGGCTTAACTGGCCGTCAATATTTGCCAATACGGGTTTCTTTC
+GCCCGGATGAAGCGCACCAGCCGCATTTCAGCGACCTGTTTGGGCAAATCATTAACGCCGGGCAAGGGGA
+AGGGCGCTATTCGGAGCTGCTGGCGATAAATCTGCTTGAGCAATTGTTACTGCGGCGCATGGAAGCGATT
+AACGAGTCGCTCCATCCACCGATGGATAATCGGGTACGCGAGGCTTGTCAGTACATCAGCGATCACCTGG
+CAGACAGCAATTTTGATATCGCCAGCGTCGCACAGCATGTTTGCTTGTCGCCGTCGCGTCTGTCACATCT
+TTTCCGCCAGCAGTTAGGGATTAGCGTCTTAAGCTGGCGCGAGGACCAACGCATTAGTCAGGCGAAGCTG
+CTTTTGAGCACTACCCGGATGCCTATCGCCACCGTCGGTCGCAATGTTGGTTTTGACGATCAACTCTATT
+TCTCGCGAGTATTTAAAAAATGCACCGGGGCCAGCCCGAGCGAGTTTCGTGCCGGTTGTGAAGAAAAAGT
+GAATGATGTAGCCGTCAAGTTGTCATAATTGGTAACGAATCAGACAATTGACGGCTTGACGGAGTAGCAT
+AGGGTTTGCAGAATCCCTGCTTCGTCCATTTGACAGGCACATTATGCAAGCATTGCTGGAACACTTTATT
+ACCCAATCCACCGTGTATTCATTGATGGCGGTGGTGTTGGTGGCCTTTCTGGAGTCGCTGGCGCTGGTCG
+GTTTGATTCTACCCGGTACGGTGCTGATGGCGGGGCTGGGAGCGCTGATTGGCAGCGGCGAGTTAAGTTT
+CTGGCACGCCTGGCTGGCAGGGATTATTGGCTGCTTGATGGGCGACTGGATTTCTTTCTGGCTGGGTTGG
+CGTTTTAAAAAGCCGTTGCATCGCTGGTCATTTCTGAAGAAAAACAAAGCACTACTTGATAAAACTGAAC
+ATGCGTTGCATCAACACAGCATGTTCACCATTCTGGTCGGTCGTTTTGTTGGCCCGACGCGTCCGCTGGT
+GCCAATGGTGGCGGGAATGCTGGATCTGCCGGTGGCTAAATTTATTACGCCGAATATTATCGGCTGCCTG
+CTGTGGCCGCCGTTTTACTTCCTGCCAGGGATTCTGGCGGGCGCGGCGATCGATATTCCTGCCGGAATGC
+AGAGCGGTGAGTTTAAATGGTTGCTGCTGGCAACAGCGGTGTTTTTGTGGGTTGGTGGCTGGCTGTGCTG
+GCGGTTATGGCGCAGCGGTAAAGCGACTGACCGTTTGAGTCATTATTTGTCCCGCGGTCGTTTGTTGTGG
+CTGACGCCGTTGATTTCTGCCATCGGCGTGGTGGCGCTGGTGGTGTTAATTCGCCACCCGTTGATGCCGG
+TGTATATCGATATTTTGCGTAAAGTGGTTGGGGTTTAGGAGATAGTCTTGTGCGGGTTGCCTGATGCGAC
+GCTTGCCGCGTCTTATCAGGCCTACAAAACGCACTACCCGTAGGTCGGATAAGGCGTTCACGCCGCATCC
+GACAGTGCATACTAACCCGTAATCCCCAATAGTGCCGAAGCACTCGCCTTACCGCTCAACAACTCATTGG
+TCATACCCTGCCAGGCGATGCGCCCGTCGGCGACTACTACCGAGCGCGTGGCGATCCGCGCCGCATCTTC
+CACGCTGTGCGACACCATCAATAGCGTCATTTTTTGCTGCTGGCAGCTCGTGCTCACCAGCGTCAACATC
+TCCTGACGTAACGCCGGATCGAGCGCAGAGAACGGTTCATCGAGCAATAAAATCGGCTGTTCGCGTACCA
+GACAACGCGCTAACGCCACTCGCTGTCGCTGACCGCCGGAAAGCTCGCCCGGTAACCGCGCCATTAAATT
+ATCAATCCCCATCTGGCGGGCGATAGCGTGCATTTTCCCCTGCTGTACCGCGTTCAGTTTCAATCCCGGA
+TTTAGCCCCAGCCCGATGTTCTGTGCGACCGTCAGGTGGCTGAACAGGTTGTTCTCCTGAAACAGCATCG
+ACACCGGACGGCGTGACGGCGGCATAGTTGTGTGATCTACGCCATCGATAGTCAGCGAACCGCTGGCTGG
+CGTCAGAAAACCGGCGATCAAATTCAGCAGGGTACTTTTACCCGCGCCGCTTGGCCCGAGGATCGCCACC
+TGCTCGCCGCGTTCCACCGTTAAGCTAAAACGCATCGGCAAATGGTGGTAAAGCCAGGTGATATCAGTCA
+GTTTTAACATTTCGCCCCGGTAGTTTTTCAATCACGGTAAACAGCAGAAAACAGAGCAGCAGCAGAATTA
+ACGCGGTGACCGCACCGTCCTGGCTGCGATAGGAGCCAATTTGCTGGTAGAGATAAAACGGCAGGGTGCG
+GAAATCATCGTTACCGAACAACGCCACCACGCCAAAATCACCAATCGACAGCACGCATGCAAAGGCCAGC
+GCCTGCGCCAGTGGACGTTTCAGGGCGCGCAGCTCCACCACTTTTAAGCGTGACCAGCCTTCAATCCCCA
+GCGACTGACATAACATGCTGTAGCGGGCGGTGATATCGCGCATCGGGTTTTCCAGCACTTTCAGCGCATA
+AGGGATCGCCATTAACGCATTGGTGAAAATCACAATGCCGTCAGCAGATTGTGGCAGGCCGATAGTGTTG
+TTGAGCAGTAAAAAGAAGCCGGTAGCCAGCACAATCCCCGGCATGGCGAGGATCAACATGCCGCTCATCT
+CCAGCACCTGACCCGCCAGCATTTTCTGCCGCGCCCGCAGTTCGCGACTGCTCCATAGCAGCATCATGGT
+CAGCACTACGCACAATACACCTGCCGCCAGCGCAATACGCAACGAGGTCCACAGCGCCTGCCACAGCACC
+GGTTGTGCCAGCACTTCCGGCAACTGGCGATTTACCCCATCGACGATCACCGCCAGTAACGGTGGCAGCA
+ACAGCAGCAGCGCCAGCACAATTAACACCGTGTCGCAAATGCGGCTATGCAGACGATCGTCCGGGTCGCG
+CCAGCCTTGCAGCAGCGTGGTGCCGGGCGCAATGGCCTTACTCAATCGCTGACTCAACAGCACCAGCCCG
+AGGCAGCACACCATCTGGAGCAGCGCCAGCATTGCCGCGCGGGCAGGATCGTAGTCGTAACTCAGCGCCT
+GATAGATTGCCAGCTCGATAGTGGTCGCCTGCGGACCGCCCCCCAGCGATAGCACGGTGGCGAAGCTGGC
+GAAACAGAGCATAAAGATAAGCGCAGCAACCGGCGGGATTTGTCGCCGTAACCACGGCCATTCGACGAAG
+CGGAAAAAATGCCAGCTACGCATCCCAAGCTGGGCGGCAAGTTGACGCTGTTCGCCGGGGATGTTTTCCA
+GTGCCTGGAGTAATAAGCGGCTCGCCATCGGCAGATTAAAAAACACATGGGCCAGCAAAATACCTTGCAG
+GCCGTAGGGCGAAAAGGTCCACTCCAGACCGAGCGATTGGCAGAGTGTTGCCAGCCAGCCCTGGCGACCA
+TAGACGCTAAGAATGCCGAAAACAGCGACCAACACCGGGAGGATCAAGGTCATTGCACACAGACGCAACA
+GCGCCAGCCGACCCGGAAAGCGCCTGCGATAGAGCGCGCGGGCGAGGAATATCGCGGGTATGACAGAGAG
+CAGTGCCGAGAGAAACGCCTGCCAGAAGGAGAAGCGCACCACATGCCACAGATAGCTGTCCTGCCAGACT
+GCCACCCAGTCATCCTGCGGCGCGTTCCACCACAGGGCGAGAAACGCCGCCAGCGCAACCGCTACCACCA
+GCGTGGTGGCGCTTACACCTGGAATTAACCAGCCGGGAATTAACGGCTGACGGCGCGTTGCCATTCGCTA
+ATCCATGCCTGACGTTGTGCCGCCACTTCGGCTGGCGTGAACTCCAACGTGGTTGCGGGTTTGGTCAATT
+TTTCAAAACCGGCAGGCAGCGTGACGTTTGCCACCGGATACATCCAGTTGCCGGTTGGGATCGCATTCTG
+GAAAGCCGGAGAAACCATAAACTGGAGGAATTTTTGCGCCAGCTCCGGCTGCTTGCTGGCAGCGGTGCGG
+GCGGCGACTTCCACTTGCAGATAGTGACCTTCGCTGAAGTTCGCGGCGGCGTAGTTATCTTTCTTCTCTT
+CGAGAATGTGATAAGCCGGAGAGGTGGTGTAACTCAGTACCAGATCGCTTTCACCTTTTAAAAACAGGCC
+GTAGGCTTCGCTCCAGCCTTTGGTGACCGTGACCGTTTTCTTCGCCAGTTTCTGCCAGGCTTGTGGGGCG
+TCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGAT
+AAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGTTTTTCAGTTTGTT
+CTTGTCATAAACGAAGGCGAAGTAGCCATAATCAAACGGTACGAAAGTGTCATTATTCCAGCCGCCGGGA
+ACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAACAGGT
+TGTTATCCAGCCCCAGCACCACATCGGCTTTACTGTTTTTGCCTTCCATCCGTAGACGGTTGAGAAGCGA
+AACGCCATCTTCCAGCGCCACCAGTTTCAGTTCGCAATTACAGTCGGCTTCAAAGGCTTTTTTAACCACC
+GGACCAGGCCCCCAGTCGGCGGCGAAGGAATCGTAGGTATAAACAGTCAGAACGGGTTTAGCGAAAACGG
+GCGCTGTGCACAGCAACAGCAGGGGCAGACATTTTTTTAACACTTTGCACCTCAAAAAAGAGTGGCAAAG
+GACTTGAGAAGGAGCCTCAAATCCCTTCGCCGGCGTTATCCGGATCAGGTTCGACGGGTATTTTCTCAGC
+GCACGCGTACGCGTGGCACCCCGTTGAGAACGGCGTTAGTGTAGTGATTTTGTTATCAACCAGCAATCAT
+GGATCCGGTGGCGCAAACCACGCTGATTTAAAATCGAACCAGCCGAGGGTATTCATGCGCAGGCCGCGCA
+TACTGCGTTGCCCCTGAATGATCAGCCAGTGGTGCAATAATGGCACCATCGCTTTGCTGGCGACCAGTTG
+CTGGCACCAGTTCGCCAGATTCATCTCGCCATTGCGCCAGCGAGCAGCGTCGGCTTGCCAGTCAATGGGA
+ATGCAATGTTGTAGCAGTGGCACTTCGCATAAATGTGCGAAAACAGAGAAGTCCAGCGGCAGGGTAAAGT
+TGGCGCTGTTTAGCCAGATATCACTTTCGATCTCTCCTGTATGCCACTGATCGTAGTCGATCTCTTTGAT
+TTTCAGCGTGACCTGGTGACTTGCCAGAATCTGCTGCATGATCCCGGCAATCACCCGATGCTCACTGTGA
+TCCTGATAAAAGGTTAGGGTGAGGCTTTCCAGGCCAGCCGGTTTTTCGCTCTTTATGGTGCGGGCATGGT
+GCCAACGGGGGAGCAGTCCATAAGCCGGGAACCACAGTTGCTGGTACTGTTCCTCAGCGAAATAGACCAG
+ATTAGTTGGAGAAAGCACATAGCTTACCCAGTCCCTGACTTGCTGATTCGCCCCGCGATGGGTGCGGCTG
+TCGAACAGTAAATAGTAGCAACCTTCCTCCAGGCGGCTTTCAATCTCTTTTTCCTCGCCCTGTGGACCTT
+TTAGCATCAGCCCTCCGGCTGGCTCGTCGGCAATTTCCGGCAGAACCCAGACGTTAACTTCGTCGATTAA
+TGCCCGGTAACCGAAGAAGTCATCGAATGCCTGAATTTTCAGTTGATTGGTGCTGTTGCGAATCACCGCA
+TACGGACCGGTGCCGATGGGATGGCTGGCAAAGTTACTGAGGGTTTCCCATTCGCGCGGCAGGATCATCG
+CCGGAACTTGCCCCAGCAGTAACGGTAACCAGCGGTCCGGTTGCGTGAGATGGATATCCAGCGTCCAGGG
+CGTCGGCGACACAATGTCAGCAATATGCGAATAGAGCGGCAGCGTATTGATTCGTTTTAAAGAGGCGATC
+ACATCGTCCATTTCCAGTTCACGACCATGGTGAAAATGGACTCCTGGACGCAAAAAGAAACGCCAGTGAA
+GCGGTGAAATTTGCTGCCAGTGGTGGGCGATGTCTGCTTCCAGTTCCCCATTTTCCTCATTTATGCGCGT
+TAGCGAACTGAAGATTTGCCGGGCGATATGGGTTTCGGAACGGCGCAATGCGCTGCCAGGTAGCAGATTA
+CGCAACGGACGATAGTAGAGCACGCGCAGGATGTGCCGCCCCTGGCGGAAGCTGCGGCCCAGATGAGAAA
+CCAGCATTTGCCGCACAGTCGCTTTGTCGCCAACCAACTGCACCAGTTGATCGATACGATCCTGCTCCAG
+CAGGTCTTCCGCCCGCTGTTGCTGAAGCGCCAGCCCGGTATAGAGGAATGTCAGACGCGAGCGTTTACCG
+CGCCCGACTTCCGCTTCCCACGTCAGCCAGCCGCGATCCTGCATGGTGTTGAGCAGGGTGCGCATATGAC
+GACGCGAGCAGCTCAATAACGCTGCCAGTTCGTTGAGCGTTGTGTCCTGCGATTTACCCTCGCAGCATTG
+CCACAGGCGGATGAACTGTTGTTGCAGACGAGCAGATGGCATAAAAGGGGAACTCCTGTGCAAAAGACAG
+CAATTTTATTTTCCCTATATTAAGTCAATAATTCCTAACGATGAAGCAAGGGGGTGCCCCATGCGTCAGT
+TTTATCAGCACTATTTTACCGCGACAGCGAAGTTGTGCTGGTTGCGTTGGTTAAGCGTCCCACAACGATT
+AACCATGCTTGAAGGACTGATGCAGTGGGATGACCGCAATTCTGAAAGTTGACTTGCCTGCATCATGTGT
+GACTGAGTATTGGTGTAAAATCACCCGCCAGCAGATTATACCTGCTGGTTTTTTTTATTCTCGCCGCGCT
+AAAAAGGGAACGTATGATCTGGATAATGACGATGGCTCGCCGTATGAACGGTGTTTACGCGGCATTTATG
+CTGGTCGCTTTTATGATGGGGGTGGCCGGGGCGCTACAGGCTCCTACATTGAGCTTATTTCTGAGTCGTG
+AGGTTGGCGCGCAACCTTTCTGGATCGGCCTCTTTTATACGGTGAATGCTATTGCTGGGATCGGCGTAAG
+CCTCTGGTTGGCAAAACGTTCTGACAGTCAGGGCGATCGGCGAAAACTGATTATATTTTGCTGTTTGATG
+GCTATCGGCAATGCGCTATTGTTTGCATTTAATCGTCATTATCTGACGCTTATCACCTGTGGTGTGCTTC
+TGGCATCTCTGGCCAATACGGCAATGCCACAGTTATTTGCTCTGGAGCGGGAATATGCGGATAACTCGGC
+GCGAGAAGTGGTGATGTTTAGCTCGGTGATGCGTGCGCAGCTTTCTCTGGCATGGGTTATCGGTCCACCG
+TTGGCCTTTATGCTGGCGTTGAATTACGGCTTTACGGTGATGTTTTCGATTGCCGCCGGGATATTCACAC
+TCAGTCTGGTATTGATTGCATTTATGCTTCCGTCTGTGGCGCGGGTAGAACTGCCGTCGGAAAATGCTTT
+ATCAATGCAAGGTGGCTGGCAGGATAGTAACGTACGGATGTTATTTGTCGCCTCGACGTTAATGTGGACC
+TGCAACACCATGTACATTATTGATATGCCGTTGTGGATCAGTAGCGAGTTAGGATTGCCAGACAAACTGG
+CGGGTTTCCTGATGGGGACGGCAGCTGGACTGGAAATACCAGCAATGATTCTGGCTGGCTACTATGTCAA
+ACGTTATGGTAAGCGGCGAATGATGGTCATAGCAGTGGCGGCAGGAGTACTGTTTTACACCGGATTGATT
+TTCTTTAATAGCCGTATGGCGTTGATGACGCTGCAACTTTTTAACGCTGTATTTATCGGCATTGTTGCGG
+GTATTGGGATGCTATGGTTTCAGGATTTAATGCCTGGAAGAGCGGGGGCAGCTACCACCTTATTTACTAA
+CAGTATTTCTACCGGGGTAATTCTGGCTGGCGTTATTCAGGGAGCAATTGCACAAAGTTGGGGGCACTTT
+GCTGTCTACTGGGTAATTGCGGTTATTTCTGTTGTCGCATTATTTTTAACCGCAAAGGTTAAAGACGTTT
+GATGACGTGGACGATAGCGGAAAGCCCGGTCATTTGACCGGGCAAGGGGATTAATTCATAAACGCAGGTT
+GTTTTGCTTCATAAGCGGCAATGGCGTCGTCGTGCTGCAAGGTAAGCCCAATACTGTCCAGACCGTTCAT
+CATGCAGTGGCGGCGGAAGGCATCGATGGTAAAGCGATAGGTTTTCTCTCCCGCTTTCACCTCTTGCGCT
+TCCAGATCCACGTCGAAATGGATCCCCGGATTAGCTTTCACCAGCGCAAACAGTTCGTCCACTTCTGCAT
+CGCTTAATTTCACCGGCAGCAGCTGGTTGTTAAAGCTATTGCCGTAGAAGATGTCAGCAAAACTCGGCGC
+AATCACCACTTTAAAACCGTAGTCGGTCAATGCCCAGGGCGCGTGCTCACGCGAAGAGCCACAGCCGAAG
+TTTTCTCGTGCCAGCAAAATGGAAGCGCCCTGATACTGCGGGAAGTTCAGCACGAAGTCCGGGTTTGGCT
+GTTGGCCTTTTTCATCCAGAAAACGCCAGTCGTTAAACAGATGCGCGCCAAAACCCGTACGGGTCACTTT
+CTGCAAAAACTGTTTCGGGATGATTGCATCGGTATCGACATTGGCGGCATCCAGCGGAACCACCAGGCCT
+GTGTGTTTGATAAATTTCTCTGCCATGGTGTGCTCCTTATTTAATGTTGCGAATGTCGGCGAAATGTCCG
+GTCACAGCAGCAGCGGCAGCCATTGCCGGGCTGACCAGATGCGTGCGCCCGCCGCGCCCCTGGCGGCCTT
+CAAAGTTACGGTTGCTGGTGGAGGCACAACGTTCGCCCGGATTCAGACGGTCGTTGTTCATCGCCAGACA
+CATTGAGCAGCCAGGCAAGCGCCATTCAAAACCGGCTTCAATAAAGATTTTATCCAGACCTTCCGCTTCC
+GCCTGGGCTTTTACCGGGCCAGAGCCGGGAACCACCAGTGCCTGCACGCCTGGCGCGACTTTTCGCCCTT
+TGGCGATCTCCGCTGCCGCGCGTAAATCTTCAATGCGCGAGTTGGTACAGGAACCGATAAACACTTTGTC
+GATAGCCACTTCGGTCAGCGGAATACCCGGTTTCAGCCCCATATAGGCCAGCGCTTTTTCTGCCGACGCG
+CGTTCAACCGGATCGGCAAACGAAGCCGGATCGGGAATATTGTCGTTCACGGAAATCACCTGGCCGGGAT
+TGGTGCCCCAGGTGACCTGCGGTGAAATTTCTTCTGCTTGCAGAGTGACAACGGTATCGAAAGTTGCGCC
+TTCGTCGGTTTGCAGGGTTTTCCAGTAGGCAACGGCGTCGTCGAAATCTTTGCCTTTCGGCGCATGCAGA
+CGGCCTTTGACATAGTTAAAGGTGGTTTCGTCCGGTGCAACCAGACCGGCTTTTGCGCCCATTTCGATTG
+CCATATTGCACAGGGTCATACGACCTTCCATGCTTAAATCACGGATTGCTTCGCCGCAAAACTCCACCAC
+ATGCCCGGTGCCGCCTGCGCTACCGGTTTTACCGATAATTGCCAGCACGATATCTTTTGCGGTAATGCCC
+GGCGCGGCTTTGCCCTGGACTTCAATTTTCATGGTTTTTGCGCGGCCCTGTTTCAGGGTTTGCGTTGCCA
+GTACGTGTTCAACTTCGGAAGTGCCGATACCAAAGGCCAGTGCGCCAAACGCGCCGTGGGTGGCGGTATG
+CGAGTCGCCGCAGACAATGGTCATCCCCGGCAAGGTGACGCCCTGTTCCGGCCCCATTACGTGGACGATC
+CCCTGATACGGGTGATTCAGGTCATACAGTTCGACGCCAAATTCTTTGCAGTTTTTGATCAGTTCCTGCA
+TCTGGATACGCGCCATTTCACCGCAGGCATTAATGTCTTTGGTCTGGGTAGAGACGTTGTGATCCATGGT
+AGCGAAGGTTTTGCCCGGCTGACGTACCGGGCGACCGTGGGCGCGCAGACCATCGAACGCCTGCGGTGAG
+GTCACTTCATGCACCAGGTGGCGGTCGATATATAACAGTGGGGTTTCGTTTTCGGCTTCGTACACAACGT
+GAGCGTCGAACAATTTTTCGTATAACGTCTTAGCCATGATTACACCCCTTCTGCTACATAGCGGGCAATG
+ATATCGCCCATTTCATCGGTACTAACGGCGGCAGCGCCACGGGCTAAATCCCCGGTGCGAATGCCTTCTT
+CTAATGCGCGGTTAATGGCGCGTTCAATGGCGCAAGCCGCATCATCGGCATCCAGGCTGTAACGCAGCAG
+CAGTGCCAGCGAAAGGATTTGTGCAATCGGGTTGGCGATGTTTTTGCCTGCGATATCTGGTGCCGAGCCG
+CCCGCCGGTTCATACAGTCCAAAACCTTGCTCGTTCAGGCTGGCGGAAGGCAACATCCCCATCGAGCCAG
+TGATCATTGCGCACTCGTCAGACAGAATGTCGCCAAACAGGTTGGAGCACAGCAGAACGTCAAACTGTGA
+TGGATCTTTAATCAGCTGCATGGTGGCGTTGTCGATGTACATATGCGCCAGTTCGACATCCGGGTATTCC
+GTGGCGATCTCGTTAACGATCTCCCGCCATAAAATAGAGGATTGCAGCACGTTGGCTTTATCGATCGACG
+TCACTTTGTGGCGACGCTTGCGAGCAGATTCAAACGCGATGCGGGCGATACGTTCGATCTCAAAACGGTG
+ATACACCTCGGTATCAAAGGCTTTTTCATATTGTCCGCTACCTTCGCGGCCTTTTGGCTGACCGAAATAG
+ATGCCGCCGGTCAGTTCGCGCACACACAGGATGTCGAAGCCGTTTGCGGCAATGTCTGCACGCAGCGGAC
+AGAATGCTTCCAGCCCCTGATACAGTTTTGCCGGGCGCAGGTTGCTGAATAATTTGAAGTGCTTACGCAG
+AGGCAGCAGCGCGCCGCGTTCTGGTTGCTGGTCTGGTGGTAAATGTTCCCACTTCGGGCCGCCTACCGAG
+CCAAACAGCACGGCATCGGCTTGCTCACAACCTTCAACCGTCGCAGGCGGCAGTGGTTGCCCGTGGTTAT
+CAATGGCTGCGCCGCCTACATCGTAATGGCTGGTGGTGATGCGCATCGCAAAGCGGTTGCGCACGGCATC
+CAGCACTTTCAGCGCCTGGGTCATCACTTCCGGACCAATACCGTCCCCCGGCAATACGGCAATATGGTAA
+TTCTTCGACATCACACGGTTTCCTTGTTGTTTTCGTTGTGTTGAGCTTTGCGTTGCAACTCTTTTTCGAC
+TTCTGCGGCACGCCAGATATTGTTCAGAACGTGCACCATGGCTTTGGCAGATGACTCGACAATATCGGTA
+GCCAGGCCGACGCCGTGGAAGCGGCGACCGTTGTAGTTAGCGACGATATCCACCTGACCCAGCGCATCTT
+TACCGTGGCCTTTGGCGGTCAGGCTGTATTTCACCAGTTCGACGTTATATTCAGTGATGCGGTTAATTGC
+CTGATAGACGGCATCGACCGGACCGTTACCGTTGGCGGCTTCTGCTTTGACTTCTTCGCCACAGGCCAGT
+TTGACGGCGGCGGTGGCGATATCGTTAGAGCCAGACTGCACGCTGAAGTAATCCAGACGGAAATGCTCCG
+GCTCTTCTTGCTGCTTACCGATGAAGGCCAGCGCCTCCAGATCGTAATCAAACACCTGACCTTTTTTGTC
+CGCCAGCTTCAGGAAAGCATCGTACAAATTGTCTAAATTATATTCACTTTCTTTATACCCCATCTCATCC
diff --git a/network/wwwblast/db/test_na_db.nhr b/network/wwwblast/db/test_na_db.nhr
new file mode 100644
index 00000000..a0eb7d17
--- /dev/null
+++ b/network/wwwblast/db/test_na_db.nhr
@@ -0,0 +1 @@
+gnl|BL_ORD_ID|0 gi|1786181|gb|AE000111|ECAE000111 Escherichia coli , thrL, thrA, thrB, thrC, yaaA, yaaJ, talB, mog, yaaH genes from bases 1 to 10596 (section 1 of 400) of the complete genomegnl|BL_ORD_ID|1 gi|1786192|gb|AE000112|ECAE000112 Escherichia coli , htgA, yaaI, dnaK, dnaJ, yi81_1, yi82_1, gefL, nhaA, nhaR, insB_1, insA_1 genes from bases 10539 to 20717 (section 2 of 400) of the complete genomegnl|BL_ORD_ID|2 gi|1786217|gb|AE000114|ECAE000114 Escherichia coli , caiF, caiE, caiD, caiC, caiB, caiA, caiT, fixA, fixB, fixC, fixX, yaaU genes from bases 34087 to 47220 (section 4 of 400) of the complete genomegnl|BL_ORD_ID|3 gi|1786230|gb|AE000115|ECAE000115 Escherichia coli , yabF, kefC, folA, apaH, apaG, ksgA, pdxA, surA, imp genes from bases 47163 to 57264 (section 5 of 400) of the complete genomegnl|BL_ORD_ID|4 gi|1786240|gb|AE000116|ECAE000116 Escherichia coli , yabH, yabP, yabQ, yabO, hepA, polB, araD, araA, araB genes from bases 57207 to 70245 (section 6 of 400) of the complete genomegnl|BL_ORD_ID|5 gi|1786250|gb|AE000117|ECAE000117 Escherichia coli , araC, yabI, yabJ, yabK, tbpA, yabN, yabM, leuD, leuC, leuB, leuA genes from bases 70188 to 83603 (section 7 of 400) of the complete genome
\ No newline at end of file
diff --git a/network/wwwblast/db/test_na_db.nin b/network/wwwblast/db/test_na_db.nin
new file mode 100644
index 00000000..14ee5ea0
--- /dev/null
+++ b/network/wwwblast/db/test_na_db.nin
diff --git a/network/wwwblast/db/test_na_db.nsq b/network/wwwblast/db/test_na_db.nsq
new file mode 100644
index 00000000..92716cc0
--- /dev/null
+++ b/network/wwwblast/db/test_na_db.nsq
diff --git a/network/wwwblast/discontiguous.html b/network/wwwblast/discontiguous.html
new file mode 100644
index 00000000..b0e00d9d
--- /dev/null
+++ b/network/wwwblast/discontiguous.html
@@ -0,0 +1,97 @@
+<HTML>
+<TITLE> Discontiguous Mega BLAST </TITLE>
+<BODY>
+<H1>
+What is discontiguous Mega BLAST? 
+</H1>
+<PRE>
+
+This version of Mega BLAST is designed specifically for comparison of diverged 
+sequences, especially sequences from different organisms, which have alignments 
+with low degree of identity, where the original Mega BLAST is not very 
+effective. The major difference is in the use of the 'discontiguous word' 
+approach to finding initial offset pairs, from which the gapped extension is 
+then performed.
+
+Both Mega BLAST and all previous versions of nucleotide-nucleotide BLAST look 
+for exact matches of certain length as the starting points for gapped 
+alignments. When comparing less conserved sequences, i.e. when the expected 
+share of identity between them is e.g. 80% and below, this traditional approach 
+becomes much less productive than for the higher degree of conservation. 
+Depending on the length of the exact match to start the alignments from, it 
+either misses a lot of statistically significant alignments, or on the contrary 
+finds too many short random alignments. 
+
+According to [1], as well as our own probability simulations, it turns out that 
+if initial 'words' are based not on the exact match, but on a match of a certain
+set of nonconsecutive positions within longer segments of the sequences, the 
+productivity of the word finding algorithm is much higher. This way fewer words 
+are found overall, but more of them end up producing statistically significant 
+alignments, than in the case of contiguous words of the same, and even shorter 
+length than the number of matched positions in the discontiguous word.
+
+As an example, we can define a pattern (template) of 0s and 1s of length e.g. 
+21:
+100101100101100101101. For each pair of offsets in the query and subject 
+sequences that are being compared, we compare the 21 nucleotide segments in 
+these sequences ending at these offsets, and require only those positions in 
+those segments to match that correspond to the 1s in the above template.
+
+There are several advantages in using this approach. First, the conditional 
+probabilities of finding word hits satisfying discontiguous templates given the 
+expected identity percentage in the alignments between two sequences, are higher
+than for contiguous words with the same number of positions required matched. 
+If two word hits are required to initiate a gapped extension, the effect
+of the discontiguous word approach is even larger. In both cases higher 
+sensitivity is achieved because there is less correlation between successive
+words as the database sequence is scanned across the query sequence.
+Second, when comparing coding sequences, the conservation of the 
+third nucleotides in every codon is not essential, so there is no need to 
+require it when matching initial words. This implies the advantage of using 
+templates based on the '110' pattern, which are called 'coding'.
+Finally, to achieve even higher sensitivity, one might combine two different 
+discontiguous word templates and require any one of them to match at a given
+position to qualify it for the initial word hit. 
+
+The following options specific to this approach are supported:
+
+Template length: 16, 18, 21.
+Word size (i.e. number of 1s in the template): 11, 12
+Template type: coding, non-coding.
+Require two words for extension: yes/no.
+
+The 'coding' templates are based on the 110 pattern, although more 0s are 
+required for most of them, so some of the patterns become 010 or 100. These are 
+the most effective for comparison of coding regions.
+
+The non-coding templates attempt to minimize the correlation between successive 
+words, when the database sequence is shifted by 4 positions against the query 
+sequence. This means more 1s are concentrated at the ends of the template (at 
+least 3 on each side). 
+
+When the option to require two words for extension is chosen, two word hits 
+matching the template must be found within a distance of 50 nucleotides of one
+another.
+
+Below are the exact discontiguous word template patterns for different combinations 
+of word sizes and lengths:
+
+   W = 11, t = 16, coding:     1101101101101101
+   W = 11, t = 16, non-coding: 1110010110110111
+   W = 12, t = 16, coding:     1111101101101101
+   W = 12, t = 16, non-coding: 1110110110110111
+   W = 11, t = 18, coding:     101101100101101101
+   W = 11, t = 18, non-coding: 111010010110010111
+   W = 12, t = 18, coding:     101101101101101101
+   W = 12, t = 18, non-coding: 111010110010110111
+   W = 11, t = 21, coding:     100101100101100101101
+   W = 11, t = 21, non-coding: 111010010100010010111
+   W = 12, t = 21, coding:     100101101101100101101
+   W = 12, t = 21, non-coding: 111010010110010010111
+
+[1] Ma, B., Tromp, J., Li, M., "PatternHunter: faster and more sensitive 
+homology search", Bioinformatics 2002 Mar;18(3):440-5
+
+</PRE>
+</BODY>
+</HTML>
diff --git a/network/wwwblast/docs/blast_databases.html b/network/wwwblast/docs/blast_databases.html
new file mode 100644
index 00000000..90b5ff61
--- /dev/null
+++ b/network/wwwblast/docs/blast_databases.html
@@ -0,0 +1,94 @@
+<head>
+<TITLE>Databases available for BLAST search</TITLE> 
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >  
+<!-- Changed by: Sergei Shavirin,  9-May-1996 -->
+</head>
+<h1 align="center">Databases available for BLAST search</h1>
+<HR>
+<h3> Peptide Sequence Databases</h3>
+<HR>
+<dl>
+<dt><b>nr</b>
+<dd>All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF
+<p>
+<dt><b>month</b>
+<dd>All new or revised GenBank CDS translation+PDB+SwissProt+PIR+PRF released in 
+the last 30 days.
+<p>
+<dt><b>swissprot</b> 
+<dd>the last major release of the SWISS-PROT protein sequence 
+database (no updates)
+<p>
+<dt><b>yeast</b>
+<dd>Yeast (Saccharomyces cerevisiae) protein sequences.
+<p>
+<dt><b>E. coli</b>
+<dd>E. coli genomic CDS translations
+<p>
+<dt>
+<b>pdb</b>
+<dd>Sequences derived from the 3-dimensional structure
+Brookhaven Protein Data Bank
+<p>
+<dt><b>kabat</b> [kabatpro]
+<dd>Kabat's database of sequences of immunological interest
+<p>
+<dt><b>alu</b>
+<dd>Translations of select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences.  It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory).  See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994) .
+<p>
+<dt>
+<hr>
+<h3>Nucleotide Sequence Databases</h3>
+<HR>
+<p>
+
+<dt><b>nr</b>
+<dd>All Non-redundant GenBank+EMBL+DDBJ+PDB sequences (but 
+no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences) 
+<p>
+<dt>
+<b>month</b>
+<dd>All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last
+30 days.
+<p>
+<dt>
+<b>dbest</b>
+<dd> Non-redundant Database of GenBank+EMBL+DDBJ EST Divisions
+<p>
+<dt><b>dbsts</b>
+<dd>Non-redundant Database of GenBank+EMBL+DDBJ STS Divisions
+<p>
+<dt>
+<b>htgs</b>
+<dd> htgs  unfinished High Throughput Genomic Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr)
+<p>
+<dt><b>yeast</b>
+<dd>Yeast (Saccharomyces cerevisiae) genomic nucleotide sequences
+<p>
+<dt><b>E. coli</b>
+<dd>E. coli genomic nucleotide sequences
+<p>
+<dt><b>pdb</b>
+<dd>Sequences derived from the 3-dimensional structure
+<p>
+<dt><b>kabat</b> [kabatnuc]
+<dd>Kabat's database of sequences of immunological interest
+<p>
+<dt><b>vector</b>
+<dd>Vector subset of GenBank(R), NCBI, in ftp://ncbi.nlm.nih.gov/blast/db/
+<p>
+<dt><b>mito</b>
+<dd>Database of mitochondrial sequences"
+<p>
+<dt><b>alu</b>
+<dd>Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences.  It is available by anonymous FTP from ncbi.nlm.nih.gov (under the /pub/jmc/alu directory).  See "Alu alert" by Claverie and Makalowski, Nature vol. 371, page 752 (1994).
+<p>
+<dt><b>epd</b>
+<dd>Eukaryotic Promotor Database
+<p>
+<dt><b>gss</b>
+<dd>Genome Survey Sequence, includes single-pass genomic data, exon-trapped
+sequences, and Alu PCR sequences.
+</dl>
+<hr>
+
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+<TITLE> BLAST Reference Manual Pages </TITLE>
+<!-- Changed by: Sergei Shavirin,  2-Apr-1996 -->
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >
+<h1 align = center>BLAST HELP MANUAL</h1>
+<HR>
+
+<h3>DESCRIPTION</h3>
+<PRE>
+     This document describes the WWW BLAST interface.
+
+     BLAST (Basic Local Alignment Search Tool) is  the  heuristic
+     search  algorithm  employed  by the programs blastp, blastn,
+     blastx, tblastn, and tblastx; these programs ascribe  signi-
+     ficance  to  their findings using the statistical methods of
+     Karlin and Altschul (1990, 1993) with  a  few  enhancements.
+     The  BLAST  programs  were  tailored for sequence similarity
+     searching -- for example to identify  homologs  to  a  query
+     sequence.   The programs are not generally useful for motif-
+     style searching.  For a discussion of basic issues in  simi-
+     larity  searching of sequence databases, see Altschul et al.
+     (1994).
+
+     The five BLAST programs described here perform the following
+     tasks:
+
+     <b>blastp</b>    compares an amino acid query  sequence  against  a
+               protein sequence database;
+
+     <b>blastn</b>    compares a nucleotide  query  sequence  against  a
+               nucleotide sequence database;
+
+     <b>blastx</b>    compares  the  six-frame  conceptual   translation
+               products  of  a  nucleotide  query  sequence (both
+               strands) against a protein sequence database;
+
+     <b>tblastn</b>   compares  a  protein  query  sequence  against   a
+               nucleotide     sequence    database    dynamically
+               translated  in  all  six  reading   frames   (both
+               strands).
+
+     <b>tblastx</b>   compares the six-frame translations of  a  nucleo-
+               tide query sequence against the six-frame transla-
+               tions of a nucleotide sequence database.
+
+<h1>BLAST Search parameters</h1>
+<p>
+<dl>
+<dt><b><a name = histogram>HISTOGRAM</a></b>
+<dd>Display a histogram of scores for each search; default
+is yes. (See parameter H in the BLAST Manual).
+<dt><b><a name = descriptions>DESCRIPTIONS</a></b>
+<dd>Restricts the number of short descriptions of matching
+sequences reported to the number specified; default
+limit is 100 descriptions.  (See parameter V in the
+manual page).  See also EXPECT and CUTOFF.
+<dt><b><a name = alignments>ALIGNMENTS</a></b>
+<dd>Restricts database sequences to the number specified for
+which high-scoring segment pairs (HSPs) are reported;
+the default limit is 50.  If more database sequences
+than this happen to satisfy the statistical
+significance threshold for reporting (see EXPECT and
+CUTOFF below), only the matches ascribed the greatest
+statistical significance are reported.
+(See parameter B in the BLAST Manual).
+<dt><b><a name = expect>EXPECT</a></b>
+<dd>
+The statistical significance threshold for reporting
+matches against database sequences; the default value
+is 10, such that 10 matches are expected to be found
+merely by chance, according to the stochastic model
+of Karlin and Altschul (1990).  If the statistical
+significance ascribed to a match is greater than the
+EXPECT threshold, the match will not be reported.
+Lower EXPECT thresholds are more stringent, leading
+to fewer chance matches being reported.  Fractional
+values are acceptable.  (See parameter E in the BLAST
+Manual).
+<dt><b><a name = cutoff>CUTOFF</a></b>
+<dd>        
+Cutoff score for reporting high-scoring segment pairs.
+The default value is calculated from the EXPECT value
+(see above).  HSPs are reported for a database sequence
+only if the statistical significance ascribed to them
+is at least as high as would be ascribed to a lone
+HSP having a score equal to the CUTOFF value.  Higher
+CUTOFF values are more stringent, leading to fewer
+chance matches being reported.  (See parameter S in
+the BLAST Manual).  Typically, significance thresholds
+can be more intuitively managed using EXPECT.
+<dt><b><a name = matrix>MATRIX</a></b>
+<dd> 
+Specify an alternate scoring matrix for BLASTP, BLASTX,
+TBLASTN and TBLASTX.  The default matrix is BLOSUM62
+(Henikoff & Henikoff, 1992).  The valid alternative
+choices include:  PAM40, PAM120, PAM250 and IDENTITY.
+No alternate scoring matrices are available for BLASTN;
+specifying the MATRIX directive in BLASTN requests
+returns an error response.
+<dt><b><a name = strand>STRAND</a></b>
+<dd> 
+Restrict a TBLASTN search to just the top or bottom
+strand of the database sequences; or restrict a BLASTN,
+BLASTX or TBLASTX search to just reading frames on the
+top or bottom strand of the query sequence.
+<dt><b><a name = filter>FILTER</a></b>
+<dd> 
+Mask off segments of the query sequence that have
+low compositional complexity, as determined by the
+SEG program of Wootton & Federhen (Computers and
+Chemistry, 1993), or segments consisting of
+short-periodicity internal repeats, as determined
+by the XNU program of Claverie & States (Computers
+and Chemistry, 1993), or, for BLASTN, by the DUST
+ program of Tatusov and Lipman (in preparation).  
+Filtering can eliminate statistically significant but 
+biologically uninteresting reports from the blast 
+output (e.g., hits against common acidic-, basic- or 
+proline-rich regions), leaving the more biologically 
+interesting regions of the query sequence available 
+for specific matching against database sequences. <BR>
+
+Low complexity sequence found by a filter program is 
+substituted using the letter "N" in nucleotide sequence 
+(e.g., "NNNNNNNNNNNNN") and the letter "X" in protein 
+sequences (e.g., "XXXXXXXXX").  Users may turn off 
+filtering by using the "Filter" option on the "Advanced 
+options for the BLAST server" page. <BR>
+
+Filtering is only applied to the query sequence (or
+its translation products), not to database sequences.
+Default filtering is DUST for BLASTN, SEG for other
+programs. <BR>	
+
+It is not unusual for nothing at all to be masked
+by SEG, XNU, or both, when applied to sequences
+in SWISS-PROT, so filtering should not be expected to
+always yield an effect.  Furthermore, in some cases,
+sequences are masked in their entirety, indicating that
+the statistical significance of any matches reported
+against the unfiltered query sequence should be suspect.
+
+<dt><b><a name = ncbi-gi>NCBI-gi<a></b>
+<dd> 
+Causes NCBI gi identifiers to be shown in the output,
+in addition to the accession and/or locus name.	
+
+</PRE>
+<h3>SEARCH STRATEGY</h3>
+<PRE>
+
+     The fundamental unit of BLAST algorithm output is the  High-
+     scoring Segment Pair (HSP).  An HSP consists of two sequence
+     fragments of arbitrary but equal length whose  alignment  is
+     locally  maximal  and for which the alignment score meets or
+     exceeds a threshold or cutoff score.  A set of HSPs is  thus
+     defined  by  two  sequences,  a scoring system, and a cutoff
+     score; this set may be empty if the cutoff score  is  suffi-
+     ciently  high.   In  the programmatic implementations of the
+     BLAST algorithm described here, each HSP consists of a  seg-
+     ment  from  the  query  sequence  and  one  from  a database
+     sequence.  The sensitivity and speed of the programs can  be
+     adjusted  via  the standard BLAST algorithm parameters W, T,
+     and X (Altschul et al., 1990); selectivity of  the  programs
+     can be adjusted via the cutoff score.
+
+     A Maximal-scoring Segment  Pair  (MSP)  is  defined  by  two
+     sequences and a scoring system and is the highest-scoring of
+     all possible segment pairs that can be produced from the two
+     sequences.   The  statistical methods of Karlin and Altschul
+     (1990, 1993) are applicable to determining the  significance
+     of MSP scores in the limit of long sequences, under a random
+     sequence model that assumes independent and identically dis-
+     tributed  choices  for  the residues at each position in the
+     sequences.  In the programs described here,  Karlin-Altschul
+     statistics  have  been extrapolated to the task of assessing
+     the significance of HSP scores obtained from comparisons  of
+     potentially short, biological sequences.
+
+     The approach to similarity searching taken by the BLAST pro-
+     grams  is  first to look for similar segments (HSPs) between
+     the query sequence and a database sequence, then to evaluate
+     the statistical significance of any matches that were found,
+     and finally to report only  those  matches  that  satisfy  a
+     user-selectable threshold of significance.  Findings of mul-
+     tiple HSPs involving the query sequence and a  single  data-
+     base  sequence  may be treated statistically in a variety of
+     ways.  By default the programs use "Sum" statistics  (Karlin
+     and  Altschul, 1993).  As such, the statistical significance
+     ascribed to a set of HSPs may be higher than  that  ascribed
+     to any individual member of the set.  Only when the ascribed
+     significance  satisfies  the  user-selectable  threshold  (E
+     parameter) will the match be reported to the user.
+
+     The task of finding HSPs begins with identifying short words
+     of  length  W  in  the  query  sequence that either match or
+     satisfy some positive-valued threshold score T when  aligned
+     with a word of the same length in a database sequence.  T is
+     referred  to  as  the  neighborhood  word  score   threshold
+     (Altschul  et  al.,  1990).  These initial neighborhood word
+     hits act as seeds for initiating  searches  to  find  longer
+     HSPs  containing  them.   The word hits are extended in both
+     directions along each sequence for as far as the  cumulative
+     alignment  score  can  be  increased.  Extension of the word
+     hits in each direction  are  halted  when:   the  cumulative
+     alignment score falls off by the quantity X from its maximum
+     achieved value; the cumulative score goes to zero or  below,
+     due  to  the  accumulation  of  one or more negative-scoring
+     residue  alignments;  or  the  end  of  either  sequence  is
+     reached.
+</PRE>
+<h3>KARLIN-ALTSCHUL STATISTICS</h3>
+<PRE>
+
+     From Karlin and  Altschul  (1990),  the  principal  equation
+     relating  the  score  of an HSP to its expected frequency of
+     chance occurrence is:
+
+                        E = K N exp(-Lambda S)
+
+     where E is the expected frequency of chance occurrence of an
+     HSP having score S (or one scoring higher); K and Lambda are
+     Karlin-Altschul parameters; N is the product  of  the  query
+     and  database  sequence  lengths,  or the size of the search
+     space; and exp is the exponentiation function.
+
+     Lambda may be thought of as the expected increase in  relia-
+     bility  of  an  alignment associated with a unit increase in
+     alignment score.  Reliability in this case is  expressed  in
+     units  of  information,  such  as bits or nats, with one nat
+     being equivalent to 1/log(2) (roughly 1.44) bits.
+
+     The expectation E (range 0 to infinity)  calculated  for  an
+     alignment between the query sequence and a database sequence
+     can be  extrapolated  to  an  expectation  over  the  entire
+     database search, by converting the pairwise expectation to a
+     probability (range 0-1) and multiplying the  result  by  the
+     ratio of the entire database size (expressed in residues) to
+     the length of the matching database sequence.  In detail:
+
+                   E_database = (1 - exp(-E)) D / d
+
+     where D is the size of the database; d is the length of  the
+     matching  database  sequence; and the quantity (1 - exp(-E))
+     is the probability, P, corresponding to  the  expectation  E
+     for  the  pairwise  sequence  comparison.   Note that in the
+     limit of infinite E, P approaches 1; and in the limit  as  E
+     approaches  0, E and P approach equality.  Due to inaccuracy
+     in the statistical methods as they are applied in the  BLAST
+     programs, whenever E and P are less than about 0.05, the two
+     values can be practically treated as being equal.
+
+     In contrast to the random sequence  model  used  by  Karlin-
+     Altschul statistics, biological sequences are often short in
+     length -- an HSP may involve a relatively large fraction  of
+     the  query or database sequence, which reduces the effective
+     size of the 2-dimensional search space defined  by  the  two
+     sequences.   To obtain more accurate significance estimates,
+     the BLAST programs compute effective lengths for  the  query
+     and database sequences that are their real lengths minus the
+     expected length of the HSP, where the expected length for an
+     HSP is computed from its score.  In no event is an effective
+     length for the query or database sequence  permitted  to  go
+     below  1.  Thus, the effective length of either the query or
+     the database sequence is computed according to  the  follow-
+     ing:
+
+          Length_eff = MAX( Length_real - Lambda S / H , 1)
+
+     where H is the relative entropy of the target and background
+     residue  frequencies (Karlin and Altschul, 1990), one of the
+     statistics reported by the BLAST programs.  H may be thought
+     of as the information expected to be obtained from each pair
+     of aligned residues in a real alignment  that  distinguishes
+     the alignment from a random one.
+</PRE>
+<h3>SCORING SCHEMES</h3>
+<PRE>
+     The default scoring matrix used by blastp, blastx,  tblastn,
+     and  tblastx  is the BLOSUM62 matrix (Henikoff and Henikoff,
+     1992).  
+
+     Several PAM (point  accepted  mutations  per  100  residues)
+     amino  acid  scoring  matrices  are  provided  in  the BLAST
+     software distribution,  including  the  PAM40,  PAM120,  and
+     PAM250.  While the BLOSUM62 matrix is a good general purpose
+     scoring matrix and is the default matrix used by  the  BLAST
+     programs,  if  one  is  restricted to using only PAM scoring
+     matrices, then the PAM120 is recommended for general protein
+     similarity  searches  (Altschul,  1991).  The pam(1) program
+     can be used to produce PAM matrices of any desired iteration
+     from  2  to  511.   Each matrix is most sensitive at finding
+     similarities at  its  particular  PAM  distance.   For  more
+     thorough searches, particularly when the mutational distance
+     between potential homologs is unknown and  the  significance
+     of  their  similarity  may be only marginal, Altschul (1991,
+     1992) recommends performing at  least  three  searches,  one
+     each with the PAM40, PAM120 and PAM250 matrices.
+
+     In blastn, the M parameter sets the reward score for a  pair
+     of matching residues; the N parameter sets the penalty score
+     for mismatching residues.  M and  N  must  be  positive  and
+     negative integers, respectively.  The relative magnitudes of
+     M and N determines the number of nucleic  acid  PAMs  (point
+     accepted mutations per 100 residues) for which they are most
+     sensitive  at  finding  homologs.   Higher  ratios  of   M:N
+     correspond to increasing nucleic acid PAMs (increased diver-
+     gence).  The default values for M and N, respectively 5  and
+     -4,  having  a ratio of 1.25, correspond to about 47 nucleic
+     acid PAMs, or about 58 amino acid PAMs; an M:N  ratio  of  1
+     corresponds  to  30 nucleic acid PAMs or 38 amino acid PAMs.
+     At higher than about 40 nucleic acid PAMs, or 50 amino  acid
+     PAMs,  better  sensitivity at detecting similarities between
+     coding regions is expected by performing comparisons at  the
+     amino  acid  level (States et al., 1991), using conceptually
+     translated nucleotide sequences (re:  blastx,  tblastn,  and
+     tblastx).
+
+     Independent of the values chosen for M and  N,  the  default
+     wordlength  W=11  used  by  blastn  restricts the program to
+     finding sequences that share at least an 11-mer  stretch  of
+     100%  identity  with  the  query.  Under the random sequence
+     model, stretches of 11  consecutive  matching  residues  are
+     unlikely  to  occur  merely  by  chance  even  between  only
+     moderately diverged homologs.  Thus, blastn with its default
+     parameter  settings is poorly suited to finding anything but
+     very similar sequences.  If better  sensitivity  is  needed,
+     one should use a smaller value for W.
+
+     For the blastn program, it may be easy to see how  multiply-
+     ing both M and N by some large number will yield proportion-
+     ally larger alignment scores with their statistical signifi-
+     cance  remaining  unchanged.  This scale-independence of the
+     statistical significance estimates from blastn has its  ana-
+     log  in  the  scoring  matrices used by the other BLAST pro-
+     grams:  multiplying all elements in a scoring matrix  by  an
+     arbitrary  factor  will  proportionally  alter the alignment
+     scores but will not  alter  their  statistical  significance
+     (assuming  numerical precision is maintained).  From this it
+     should be clear that raw alignment  scores  are  meaningless
+     without  specific  knowledge  of the scoring matrix that was
+     used.
+</PRE>
+<h3>SCORING REQUIREMENTS</h3>
+<PRE>
+     Regardless of the scoring  scheme  employed,  two  stringent
+     criteria  must  be  met in order to be able to calculate the
+     Karlin-Altschul parameters Lambda and K.  First,  given  the
+     residue  composition  for the query sequence and the residue
+     composition assumed for the database,  the  alignment  score
+     expected  for  any  randomly  selected pair of residues (one
+     from the query sequence and one from the database)  must  be
+     negative.   Second,  given the sequence residue compositions
+     and the scoring scheme, a positive score must be possible to
+     achieve.   For  instance,  the  match reward score of blastn
+     must have a positive value; and given the assumption made by
+     blastn  that the 4 nucleotides A, C, G and T are represented
+     at equal 25% frequencies in the database, a  wide  range  of
+     value  combinations  for  M  and N are precluded from use --
+     namely those combinations where the magnitude of  the  ratio
+     M:N is greater than or equal to 3.
+</PRE>
+<h3>GENETIC CODES</h3>
+<PRE>
+     The parameter C can be set to a positive integer  to  select
+     the  genetic code that will be used by blastx and tblastx to
+     translate the query sequence.  The -dbgcode parameter can be
+     used  to select an alternate genetic code for translation of
+     the database by the programs tblastn and tblastx.   In  each
+     case,  the  default genetic code is the so-called "Standard"
+     or "Universal" genetic code.  To obtain  a  listing  of  the
+     genetic codes available and their associated numerical iden-
+     tifiers, invoke blastx or  tblastx  with  the  command  line
+     parameter C=list. Note:  the numerical identifiers used here
+     for  genetic  codes  parallel  those  defined  in  the  NCBI
+     software  Toolbox;  hence  some  numerical  values  will  be
+     skipped as genetic codes are updated.
+
+     The list of genetic codes  available  and  their  associated
+     values for the parameters C and -dbgcode are:
+
+     1 Standard or Universal
+
+     2 Vertebrate Mitochondrial
+
+     3 Yeast Mitochondrial
+
+     4   Mold,   Protozoan,   Coelenterate   Mitochondrial    and
+     Mycoplasma/Spiroplasma
+
+     5 Invertebrate Mitochondrial
+
+     6 Ciliate Macronuclear
+
+     9 Echinodermate Mitochondrial
+
+     10 Alternative Ciliate Macronuclear
+
+     11 Eubacterial
+
+     12 Alternative Yeast
+
+     13 Ascidian Mitochondrial
+
+     14 Flatworm Mitochondrial
+
+</PRE>
+<h3>P-VALUES, ALIGNMENT SCORES, AND INFORMATION</h3>
+<PRE>
+     The Expect and P-values reported for HSPs are  dependent  on
+     several factors including:  the scoring system employed, the
+     residue composition of the query sequence, an assumed  resi-
+     due  composition for a typical database sequence, the length
+     of the query sequence, and the total length of the database.
+     HSP  scores from different program invocations are appropri-
+     ate for comparison even if the  databases  searched  are  of
+     different  lengths,  as  long as the other factors mentioned
+     here do  not  vary.   For  example,  alignment  scores  from
+     searches  with  the  default  BLOSUM62  matrix should not be
+     directly compared  with  scores  obtained  with  the  PAM120
+     matrix;  and  scores produced using two versions of the same
+     PAM matrix, each created to different  scales  (see  above),
+     can  not  be meaningfully compared without conversion to the
+     same scale.
+
+     Some isolation from the many factors involved  in  assessing
+     the  statistical  significance  of  HSPs  can be attained by
+     observing the information content reported (in bits) for the
+     alignments.   While  the  information  content of an HSP may
+     change when different scoring systems are used  (e.g.,  with
+     different  PAM matrices), the number of bits reported for an
+     HSP will at least be independent of the scale to  which  the
+     scoring  matrix was generated.  (In practice, this statement
+     is not quite true, because the alignment scores used by  the
+     BLAST  programs  are integers that lack much precision).  In
+     other words, when conveying the statistical significance  of
+     an  alignment,  the  alignment  score  itself  is not useful
+     unless the specific scoring matrix that was employed is also
+     provided, but the informativeness of an alignment is a mean-
+     ingful statistic that can be  used  to  ascribe  statistical
+     significance  (a  P-value)  to  the  match  independently of
+     specific knowledge about the scoring matrix.
+</PRE>
+<h3>SAMPLE OUTPUT</h3>
+<PRE>
+     The BLAST programs all provide information  in  roughly  the
+     same  format.   First  comes (A) an introduction to the pro-
+     gram; (B) a histogram of expectations (see above) if one was
+     requested; (C) a series of one-line descriptions of matching
+     database sequences; (D) the actual sequence alignments;  and
+     finally  the parameters and other statistics gathered during
+     the search.
+
+     Sample blastp output from comparing pir|A01243|DXCH  against
+     the SWISS-PROT database is presented below.
+
+  <b>A. Program Introduction</b>
+     The introductory output provides the program name (BLASTP in
+     this  case),  the version number (1.4.6MP in this case), the
+     date the program  source  code  last  changed  substantially
+     (June  13,  1994), the date the program was built (Sept. 22,
+     1994), and a description of the query sequence and  database
+     to be searched.  These may all be important pieces of infor-
+     mation if a  bug  is  suspected  or  if  reproducibility  of
+     results is important.
+
+     The "Searching..." indicator  indicates  progress  that  the
+     program made in searching the database.  A complete database
+     search will yield 50 periods (.), or one period per database
+     sequence,  whichever  number  is  smaller.  When searching a
+     database consisting of 50 sequences or more, if  fewer  than
+     50  periods  are  displayed and the program aborted for some
+     reason, dividing the number of periods by 0.5 will yield the
+     approximate  percentage  (0-100%)  of  the database that was
+     searched before the program died.  If the program had diffi-
+     culty  making  progress  through  the  database, one or more
+     asterisks (*) may be interspersed  between  the  periods  at
+     one-minute intervals.
+
+  <b>B. Histogram of Expectations</b>
+     Shown in the output below is a histogram of the lowest (most
+     significant)  Expect  values  obtained  with  each  database
+     sequence.  This information is  useful  in  determining  the
+     numbers  of  database  sequences  that achieved a particular
+     level of statistical significance.  It indicates the  number
+     of database matches that would be reportable at various set-
+     tings for the expectation threshold (E parameter).
+
+  <b>C. One-line Summaries</b>
+     The one-line sequence descriptions and summaries of  results
+     are useful for identifying biologically interesting database
+     matches and correlating this interest with  the  statistical
+     significance  estimates.   Unless  otherwise  requested, the
+     database sequences are sorted by increasing P-value  (proba-
+     bility).   Identifiers  for the database sequences appear in
+     the first column;  then  come  brief  descriptions  of  each
+     sequence,  which may need to be truncated in order to fit in
+     the available space.  The "High Score" column  contains  the
+     score  of  the  highest-scoring HSP found with each database
+     sequence.  The "P(N)" column  contains  the  lowest  P-value
+     ascribed  to any set of HSPs for each database sequence; and
+     the "N" column displays the number of HSPs in the set  which
+     was  ascribed  the lowest P-value.  The P-values are a func-
+     tion of N, as used in Karlin-Altschul  "Sum"  statistics  or
+     Poisson  statistics, to treat situations where multiple HSPs
+     are found.  It should be noted that the highest-scoring  HSP
+     whose  score  is  reported in the "High Score" column is not
+     necessarily a member of the set of  HSPs  which  yields  the
+     lowest P-value; the highest-scoring HSP may be excluded from
+     this set on the basis of  consistency  rules  governing  the
+     grouping  of HSPs (see the -consistency option).  Numbers of
+     the form "7.7e-160" are in  scientific  notation.   In  this
+     particular  example,  the  number  being  represented is 7.7
+     times 10 to the minus 160th power.  which is  astronomically
+     close to zero.
+
+  <b>D. Alignments</b>
+     Alignments found with  the  BLAST  algorithm  are  ungapped.
+     Several  statistics  are used to describe each HSP:  the raw
+     alignment Score; the raw score converted to bits of informa-
+     tion  by  multiplying by Lambda (see the Statistics output);
+     the number of times one might Expect to see such a match (or
+     a  better one) merely by chance; the P-value (probability in
+     the range 0-1) of observing such a  match;  the  number  and
+     fraction  of  total residues in the HSP which are identical;
+     the number and fraction of residues for which the  alignment
+     scores  have positive values.  When Sum statistics have been
+     used to calculate the Expect and P-values,  the  P-value  is
+     qualified  with  the  word "Sum" and the N parameter used in
+     the Sum statistics is provided in  parentheses  to  indicate
+     the  number of HSPs in the set; when Poisson statistics have
+     been used to calculate the Expect and P-values, the  P-value
+     is qualified with the word "Poisson".  Between the two lines
+     of Query and Subject (database) sequence is a line  indicat-
+     ing  the  specific  residues which are identical, as well as
+     those which are non-identical but nevertheless have positive
+     alignment scores defined in the scoring matrix that was used
+     (the BLOSUM62 matrix in this case).   Identical  letters  or
+     residues,  when  paired with each other, are not highlighted
+     if their alignment score is negative or zero.   Examples  of
+     this  would  be  an X juxtaposed with an X in two amino acid
+     sequences, or an N juxtaposed with another N in two  nucleo-
+     tide sequences.  Such ambiguous residue-residue pairings may
+     be uninformative and thus lend no  support  to  the  overall
+     alignment being either real or random; however, the informa-
+     tiveness of these pairings is left up to  the  user  of  the
+     BLAST  programs to decide, because any values desired can be
+     specified in a scoring matrix of the user's own making.
+
+     <b>BLASTP 1.4.6MP [13-Jun-94] [Build 13:58:36 Sep 22 1994]</b>
+
+     <b>Reference:</b>  Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers,
+     and David J. Lipman (1990).  Basic local alignment search tool.  J. Mol. Biol.
+     215:403-10.
+
+     <b>Query</b> =  pir|A01243|DXCH  232 Gene X protein - Chicken (fragment)
+             (232 letters)
+
+     <b>Database:</b>  SWISS-PROT Release 29.0
+                38,303 sequences; 13,464,008 total letters.
+     Searching..................................................done
+
+
+          Observed Numbers of Database Sequences Satisfying
+          Various EXPECTation Thresholds (E parameter values)
+
+             Histogram units:      = 31 Sequences     : less than 31 sequences
+
+      EXPECTation Threshold
+      (E parameter)
+         |
+         V   Observed Counts-->
+       10000 4863 1861 |============================================================
+        6310 3002  782 |=========================
+        3980 2220  812 |==========================
+        2510 1408  303 |=========
+        1580 1105  393 |============
+        1000  712  179 |=====
+         631  533  161 |=====
+         398  372   80 |==
+         251  292   73 |==
+         158  219   50 |=
+         100  169   32 |=
+        63.1  137   18 |:
+        39.8  119    9 |:
+        25.1  110    6 |:
+        15.8  104    9 |:
+      >>>>>>>>>>>>>>>>>>>>>  Expect = 10.0, Observed = 95  <<<<<<<<<<<<<<<<<
+        10.0   95    4 |:
+        6.31   91    3 |:
+        3.98   88    1 |:
+        2.51   87    3 |:
+        1.58   84    0 |
+        1.00   84    2 |:
+
+
+                                                                          Smallest
+                                                                            Sum
+                                                                   High  Probability
+     Sequences producing High-scoring Segment Pairs:              Score  P(N)      N
+
+     sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED) (...  1191  7.7e-160  1
+     sp|P01014|OVAY_CHICK GENE Y PROTEIN (OVALBUMIN-RELATED).       949  7.0e-127  1
+     sp|P01012|OVAL_CHICK OVALBUMIN (PLAKALBUMIN).                  645  3.4e-100  2
+     sp|P19104|OVAL_COTJA OVALBUMIN.                                626  1.2e-96   2
+     sp|P05619|ILEU_HORSE LEUKOCYTE ELASTASE INHIBITOR (LEI).       216  3.7e-71   3
+     sp|P80229|ILEU_PIG   LEUKOCYTE ELASTASE INHIBITOR (LEI) (...   325  4.0e-71   2
+     sp|P29508|SCCA_HUMAN SQUAMOUS CELL CARCINOMA ANTIGEN (SCC...   439  3.5e-70   2
+     sp|P30740|ILEU_HUMAN LEUKOCYTE ELASTASE INHIBITOR (LEI) (...   211  1.3e-66   3
+     sp|P05120|PAI2_HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2, P...   176  1.8e-65   4
+     sp|P35237|PTI_HUMAN  PLACENTAL THROMBIN INHIBITOR.             473  1.3e-61   1
+     sp|P29524|PAI2_RAT   PLASMINOGEN ACTIVATOR INHIBITOR-2, T...   183  9.4e-61   4
+     sp|P12388|PAI2_MOUSE PLASMINOGEN ACTIVATOR INHIBITOR-2, M...   179  1.8e-60   4
+     sp|P36952|MASP_HUMAN MASPIN PRECURSOR.                         198  2.6e-58   4
+     sp|P32261|ANT3_MOUSE ANTITHROMBIN-III PRECURSOR (ATIII).       142  4.0e-48   5
+     sp|P01008|ANT3_HUMAN ANTITHROMBIN-III PRECURSOR (ATIII).       122  7.5e-48   5
+
+     WARNING:  Descriptions of 80 database sequences were not reported due to the
+               limiting value of parameter V = 15.
+
+
+       ... alignments with the top 8 database sequences deleted ...
+
+     >sp|P05120|PAI2_HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2, PLACENTAL (PAI-2)
+                 (MONOCYTE ARG- SERPIN).
+                 Length = 415
+
+      Score = 176 (80.2 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
+      Identities = 38/89 (42%), Positives = 50/89 (56%)
+
+     Query:     1 QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNN 60
+                  +I +LL   S D DT +VLVNA+YFKG WKT F  +     PF V   +  PVQMM +
+     Sbjct:   180 KIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLRE 239
+
+     Query:    61 SFNVATLPAEKMKILELPFASGDLSMLVL 89
+                    N+  +   K +ILELP+A      L+L
+     Sbjct:   240 KLNIGYIEDLKAQILELPYAGDVSMFLLL 268
+
+      Score = 165 (75.2 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
+      Identities = 33/78 (42%), Positives = 47/78 (60%)
+
+     Query:   155 ANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHPFLFL 214
+                  AN +G+S    L +S+  H A ++++E+G E A  TG +   +      QF ADHPFLFL
+     Sbjct:   338 ANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFL 397
+
+     Query:   215 IKHNPTNTIVYFGRYWSP 232
+                  I H  T  I++FGR+ SP
+     Sbjct:   398 IMHKITKCILFFGRFCSP 415
+
+      Score = 144 (65.6 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
+      Identities = 26/62 (41%), Positives = 41/62 (66%)
+
+     Query:    90 LPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTSVLMALGMTD 149
+                  + D  + LE +E  I ++KL +WT+ + M +  V+VY+PQ K+EE Y L S+L ++GM D
+     Sbjct:   272 IADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMED 331
+
+     Query:   150 LF 151
+                   F
+     Sbjct:   332 AF 333
+
+      Score = 61 (27.8 bits), Expect = 1.8e-65, Sum P(4) = 1.8e-65
+      Identities = 10/17 (58%), Positives = 16/17 (94%)
+
+     Query:    81 SGDLSMLVLLPDEVSDL 97
+                  +GD+SM +LLPDE++D+
+     Sbjct:   259 AGDVSMFLLLPDEIADV 275
+
+
+     WARNING:  HSPs involving 86 database sequences were not reported due to the
+               limiting value of parameter B = 9.
+
+
+     Parameters:
+       V=15
+       B=9
+       H=1
+
+       -ctxfactor=1.00
+       E=10
+
+       Query                        -----  As Used  -----    -----  Computed  ----
+       Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
+        +0      0   BLOSUM62        0.316   0.132   0.370    same    same    same
+
+       Query
+       Frame  MatID  Length  Eff.Length   E    S W   T  X     E2  S2
+        +0      0      232       232      10. 57 3  11 22    0.22 33
+
+
+     Statistics:
+       Query          Expected         Observed           HSPs       HSPs
+       Frame  MatID  High Score       High Score       Reportable  Reported
+        +0      0    62 (28.2 bits)  1191 (542.5 bits)     330         24
+
+       Query         Neighborhd  Word      Excluded    Failed   Successful  Overlaps
+       Frame  MatID   Words      Hits        Hits    Extensions Extensions  Excluded
+        +0      0      4988     5661199     1146395     4504598    10187        13
+
+       Database:  SWISS-PROT Release 29.0
+         Release date:  June 1994
+         Posted date:  1:29 PM EDT Jul 28, 1994
+       # of letters in database:  13,464,008
+       # of sequences in database:  38,303
+       # of database sequences satisfying E:  95
+       No. of states in DFA:  561 (55 KB)
+       Total size of DFA:  110 KB (128 KB)
+       Time to generate neighborhood:  0.03u 0.01s 0.04t  Real: 00:00:00
+       No. of processors used:  8
+       Time to search database:  32.27u 0.78s 33.05t  Real: 00:00:04
+       Total cpu time:  32.33u 0.91s 33.24t  Real: 00:00:05
+
+     WARNINGS ISSUED:  2
+
+</PRE>
+<h3>COPYRIGHT</h3>
+<PRE>
+     This work is in the public domain.
+
+</PRE>
+<h3>REFERENCES</h3>
+<PRE>
+
+     Altschul,  Stephen  F.  (1991).   Amino  acid   substitution
+     matrices  from an information theoretic perspective. J. Mol.
+     Biol.  219:555-65.
+
+     Altschul, S. F. (1993).  A protein alignment scoring  system
+     sensitive  at  all  evolutionary  distances.  J.  Mol. Evol.
+     36:290-300.
+
+     Altschul, S. F., M. S. Boguski, W. Gish and  J.  C.  Wootton
+     (1994).   Issues  in searching molecular sequence databases.
+     Nature Genetics 6:119-129.
+
+     Altschul, Stephen F., Warren Gish, Webb  Miller,  Eugene  W.
+     Myers,  and  David  J. Lipman (1990).  Basic local alignment
+     search tool. J. Mol. Biol.  215:403-10.
+
+     Claverie,  J.-M.  and  D.  J.  States  (1993).   Information
+     enhancement  methods for large scale sequence analysis. Com-
+     puters in Chemistry 17:191-201.
+
+     Gish, W. and D. J. States (1993).  Identification of protein
+     coding  regions by database similarity search. Nature Genet-
+     ics 3:266-72.
+
+     Henikoff, Steven and Jorga G. Henikoff (1992).   Amino  acid
+     substitution matrices from protein blocks. Proc. Natl. Acad.
+     Sci. USA 89:10915-19.
+
+     Karlin, Samuel and Stephen F. Altschul (1990).  Methods  for
+     assessing the statistical significance of molecular sequence
+     features by using general scoring schemes. Proc. Natl. Acad.
+     Sci. USA 87:2264-68.
+
+     Karlin, Samuel and Stephen F. Altschul (1993).  Applications
+     and statistics for multiple high-scoring segments in molecu-
+     lar sequences. Proc. Natl. Acad. Sci. USA 90:5873-7.
+
+     States, D. J. and W. Gish (1994).  Combined use of  sequence
+     similarity  and codon bias for coding region identification.
+     J. Comput. Biol.  1:39-50.
+
+     States, D. J., W. Gish and S. F. Altschul (1991).   Improved
+     sensitivity  of  nucleic  acid  database similarity searches
+     using application specific scoring matrices. Methods: A com-
+     panion to Methods in Enzymology 3:66-70.
+
+     Wootton, J. C. and S. Federhen (1993).  Statistics of  local
+     complexity  in  amino acid sequences and sequence databases.
+     Computers in Chemistry 17:149-163.
+
+</PRE>
+
diff --git a/network/wwwblast/docs/blast_program.html b/network/wwwblast/docs/blast_program.html
new file mode 100644
index 00000000..f8a59a59
--- /dev/null
+++ b/network/wwwblast/docs/blast_program.html
@@ -0,0 +1,36 @@
+<head>
+<title>Programs available for the BLAST search</title>
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >  
+<!-- Changed by: Sergei Shavirin,  2-Apr-1996 -->
+</head>
+<h1 align="center">Programs available for the BLAST search</h1>
+<hr>
+<p>
+The NCBI <b>BLAST</b> family of programs includes:
+<p>
+<dl>
+<dt><b>blastp</b> 
+<dd>compares an amino acid query sequence against a protein sequence 
+database
+<p>
+<dt><b>blastn</b> 
+<dd>compares a nucleotide query sequence against a nucleotide sequence 
+database
+<p>
+<dt><b>blastx</b> 
+<dd>compares a nucleotide query sequence translated in all reading frames 
+against a protein sequence database
+<p>
+<dt><b>tblastn</b> 
+<dd>compares a protein query sequence against a nucleotide sequence database 
+dynamically translated in all reading frames
+<p>
+<dt><b>tblastx</b> 
+<dd>compares the six-frame translations of a nucleotide query sequence
+against the six-frame translations of a nucleotide sequence database.
+Please note that tblastx program cannot be used with the nr database on the BLAST Web page.
+<p>
+</ul>
+<hr>
+</body>
+</html>
diff --git a/network/wwwblast/docs/color_schema.html b/network/wwwblast/docs/color_schema.html
new file mode 100644
index 00000000..5a045167
--- /dev/null
+++ b/network/wwwblast/docs/color_schema.html
@@ -0,0 +1,71 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+  <head>
+    <title>BLAST Color schema description</title>
+  </head>
+
+  <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+    <HR>
+    <CENTER><h1>BLAST Color schema description</h1></CENTER>
+    <HR>
+    <UL>
+      <LI> Color schema 1:
+        <UL>
+          <LI> masked regions in lower case
+          <LI> everything else in upper case
+        </UL>
+      <LI> Color schema 2:
+        <UL>
+          <LI> masked regions in lower case, gray letters
+          <LI> Unaligned regions in italic
+          <LI> everything else in upper case
+        </UL>
+      <LI> Color schema 3:
+        <UL>
+          <LI> No middle line.
+          <LI> Masked regions in lower case, gray letters unless identity
+          <LI> Everything else in upper case
+          <LI> Unaligned regions in italic
+          <LI> Identity shown in red color
+          <LI> Similarity shown in blue color 
+          <LI> Mismatches shown in black color 
+        </UL>
+      <LI> Color schema 4:
+        <UL>
+          <LI> No middle line.
+          <LI> Masked regions in lower case, gray letters
+          <LI> Everything else in upper case
+          <LI> Unaligned regions in italic
+          <LI> Identity shown in blue color
+          <LI> Similarity shown in brown color 
+          <LI> Mismatches shown in red color 
+        </UL>
+      <LI> Color schema 5:
+        <UL>
+          <LI> No middle line.
+          <LI> Masked regions in lower case, gray letters
+          <LI> Everything else in upper case
+          <LI> Unaligned regions in italic
+          <LI> Identity shown in red color
+          <LI> Similarity shown in blue color 
+          <LI> Mismatches shown in black color 
+        </UL>
+      <LI> Color schema 6:
+        <UL>
+          <LI> No middle line.
+          <LI> Masked regions in lower case, gray letters unless identity
+          <LI> Everything else in upper case
+          <LI> Unaligned regions in italic
+          <LI> Identity shown in red bold color
+          <LI> Similarity shown in blue color 
+          <LI> Mismatches shown in gray color 
+        </UL>
+    </UL>
+    <HR>
+    <!-- Created: Tue May 16 13:07:50 EDT 2000 -->
+    <!-- Created by: <a href="mailto:shavirin@ncbi.nlm.nih.gov">Sergey Shavirin</a> -->
+    <!-- hhmts start -->
+Last modified: Tue May 16 16:18:28 EDT 2000
+<!-- hhmts end -->
+  </body>
+</html>
diff --git a/network/wwwblast/docs/composition.html b/network/wwwblast/docs/composition.html
new file mode 100644
index 00000000..ad890e86
--- /dev/null
+++ b/network/wwwblast/docs/composition.html
@@ -0,0 +1,36 @@
+<HTML>
+<head>
+<TITLE>Composition based statistics</TITLE>
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >
+<!-- Changed by: Sergei Shavirin,  7-Aug-2000 -->
+</head>
+<h1 align="center">Composition based statistics</h1>
+<P>
+  BLAST and PSI-BLAST now permit calculated E-values to take into
+account the amino acid composition of the individual database
+sequences involved in reported alignments.  This improves E-value
+accuracy, thereby reducing the number of false positive results.
+<P>
+  The improved statistics are achieved with a scaling procedure [1,2]
+which in effect employs a slightly different scoring system for each
+database sequence.  As a result, raw BLAST alignment scores in general
+will not correspond precisely to those implied by any standard
+substitution matrix.  Furthermore, identical alignments can receive
+different scores, based upon the compositions of the sequences they
+involve. The improved statistics are now used by default for all rounds
+of searching on the PSI-BLAST page, but not on the BLAST page.
+Therefore, if one uses default settings, the results of the first
+round of searching will be different on the BLAST and PSI-BLAST pages.
+
+<P>
+  In addition adjustments have been made to two PSI-BLAST parameters:
+the pseudocount constant default has been changed from 10 to 7, and
+the E-value threshold for including matches in the PSI-BLAST model
+has been changed from 0.001 to 0.002.
+<P>
+
+1. <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=9254694&dopt=Abstract">Altschul, S.F. et al. (1997) Nucl. Acids Res. 25:3389-3402.</a><BR>
+2. <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10745990&dopt=Abstract">Sch&auml;ffer, A.A. et al. (1999) Bioinformatics 15:1000-1011.</a>
+
+</BODY>
+</HTML>
diff --git a/network/wwwblast/docs/fasta.html b/network/wwwblast/docs/fasta.html
new file mode 100644
index 00000000..443a2cae
--- /dev/null
+++ b/network/wwwblast/docs/fasta.html
@@ -0,0 +1,70 @@
+<TITLE> FASTA format description </TITLE>
+<!-- Changed by: Sergei Shavirin,  2-Apr-1996 -->
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >  
+<h1>FASTA format description</h1>
+<HR>
+<p>
+<dd>A sequence in FASTA format begins with a single-line description, 
+followed by lines of sequence data.  The description line is 
+distinguished from the sequence data by a greater-than (">") symbol 
+in the first column.  It is recommended that all lines of text be 
+shorter than 80 characters in length. An example sequence in FASTA 
+<BR>format is:
+
+<PRE>
+
+>gi|532319|pir|TVFV2E|TVFV2E envelope protein
+ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT
+QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC
+HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK
+MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK
+TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF
+APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL
+LAAVEAQQQMLKLTIWGVK
+
+</PRE>
+
+<dd> Sequences are expected to be represented in the standard 
+IUB/IUPAC amino acid and nucleic acid codes, with these 
+exceptions:  lower-case letters are accepted and are mapped 
+into upper-case; a single hyphen or dash can be used to represent 
+a gap of indeterminate length; and in amino acid sequences, U and *
+are acceptable letters (see below).  Before submitting a request, 
+any numerical digits in the query sequence should either be 
+removed or replaced by appropriate letter codes (e.g., N for 
+unknown nucleic acid residue or X for unknown amino acid residue).
+<BR>
+The nucleic acid codes supported are:
+<PRE>
+        A --> adenosine           M --> A C (amino)
+        C --> cytidine            S --> G C (strong)
+        G --> guanine             W --> A T (weak)
+        T --> thymidine           B --> G T C
+        U --> uridine             D --> G A T
+        R --> G A (purine)        H --> A C T
+        Y --> T C (pyrimidine)    V --> G C A
+        K --> G T (keto)          N --> A G C T (any)
+                                  -  gap of indeterminate length
+</PRE>
+
+For those programs that use amino acid query sequences (BLASTP 
+and TBLASTN), the accepted amino acid codes are:
+<PRE>
+
+    A  alanine                         P  proline
+    B  aspartate or asparagine         Q  glutamine
+    C  cystine                         R  arginine
+    D  aspartate                       S  serine
+    E  glutamate                       T  threonine
+    F  phenylalanine                   U  selenocysteine
+    G  glycine                         V  valine
+    H  histidine                       W  tryptophan
+    I  isoleucine                      Y  tyrosine
+    K  lysine                          Z  glutamate or glutamine
+    L  leucine                         X  any
+    M  methionine                      *  translation stop
+    N  asparagine                      -  gap of indeterminate length
+</PRE>
+<HR>
+
+
diff --git a/network/wwwblast/docs/files.html b/network/wwwblast/docs/files.html
new file mode 100644
index 00000000..944a45ba
--- /dev/null
+++ b/network/wwwblast/docs/files.html
@@ -0,0 +1,19 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+  <head>
+    <title>Files of standalone WWW BLAST server </title>
+  </head>
+
+  <body>
+    <h2>Files of standalone WWW BLAST server </h2>
+
+
+
+    <hr>
+    <address><a href="mailto:shavirin@ncbi.nlm.nih.gov">Sergei Shavirin</a></address>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Thu Mar 16 16:41:33 EST 2000
+<!-- hhmts end -->
+  </body>
+</html>
diff --git a/network/wwwblast/docs/filtered.html b/network/wwwblast/docs/filtered.html
new file mode 100644
index 00000000..e1bcda3a
--- /dev/null
+++ b/network/wwwblast/docs/filtered.html
@@ -0,0 +1,49 @@
+<TITLE>Low complexity filtering</TITLE>
+<!-- Changed by: Sergei Shavirin,  2-Apr-1996 -->
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >  
+<h1>Low complexity filtering</h1>
+
+<p>
+<dd>The server filters your query sequence for low compositional
+complexity regions by default.  Low complexity regions commonly give 
+spuriously high scores that reflect compositional bias rather than 
+significant position-by- position alignment.  Filtering can elminate 
+these potentially confounding matches (e.g., hits against proline-rich 
+regions or poly-A tails) from the blast reports, leaving regions whose 
+blast statistics reflect the specificity of their pairwise alignment.
+Queries searched with the blastn program are filtered with DUST.  Other
+programs use SEG.  
+</p>
+
+<p>
+Low complexity sequence found by a filter program is substituted using the 
+letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") and the letter "X" 
+in protein sequences (e.g., "XXXXXXXXX").  Users may turn off filtering by 
+using the "Filter" option on the "Advanced options for the BLAST server" page. 
+</p>
+
+<HR> 
+
+<h3>Reference for the DUST program:</h3>
+ 
+<dd><b>Tatusov, R. L.</b> and <b>D. J. Lipman</b>, in preparation.
+
+<dd><b>Hancock, J. M.</b> and <b>J. S. Armstrong</b> (1994). SIMPLE34: an 
+improved and enhanced implementation for VAX and Sun computers of the 
+SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide 
+sequences.  Comput Appl Biosci 10:67-70. 
+
+<h3>Reference for the SEG program:</h3>
+<dd><b>Wootton, J. C.</b> and <b>S. Federhen</b> (1993).  Statistics of
+local complexity  in  amino acid sequences and sequence databases.
+Computers in Chemistry 17:149-163.
+
+<dd><b>Wootton, J. C.</b> and <b>S. Federhen</b> (1996).  Analysis of 
+compositionally biased regions in sequence databases.  Methods in Enzymology
+266: 554-571.
+
+<h3>Reference for the role of filtering in search strategies:</h3>
+<dd><b>Altschul, S. F.</b>, <b>M. S. Boguski</b>, <b>W. Gish</b>, 
+<b>J. C. Wootton</b> (1994). Issues in searching molecular sequence 
+databases. Nat Genet 6: 119-129.<BR>
+<HR>
diff --git a/network/wwwblast/docs/full_options.html b/network/wwwblast/docs/full_options.html
new file mode 100644
index 00000000..702c0eb4
--- /dev/null
+++ b/network/wwwblast/docs/full_options.html
@@ -0,0 +1,79 @@
+<html>
+  <head>
+    <title>NCBI BLAST Advanced Options</title>
+  </head>
+
+  <body bgcolor = "white">
+      <h1>Full list of the BLAST Advanced options</h1>
+    <UL>
+      <LI> <a href = "#blastn">blastn</a> 
+      <LI> <a href = "#blastp">blastp</a> 
+      <LI> <a href = "#blastx">blastx</a> 
+      <LI> <a href = "#tblastn">tblastn</a> 
+    </UL>
+<HR>
+    <h3><a name = blastn><FONT color="green">
+        BLASTN Program Advanced Options</FONT></a></h3>
+<PRE>
+  -G  Cost to open a gap [Integer]
+    default = 5
+  -E  Cost to extend a gap [Integer]
+    default = 2
+  -q  Penalty for a mismatch in the blast portion of run [Integer]
+    default = -3
+  -r  Reward for a match in the blast portion of run [Integer]
+    default = 1
+  -e  Expectation value (E) [Real]
+    default = 10.0
+  -W  Word size, default is 11 for blastn, 3 for other programs.
+  -v  Number of one-line descriptions (V) [Integer]
+    default = 100
+  -b  Number of alignments to show (B) [Integer]
+    default = 100
+
+
+</PRE>
+<HR>
+    <h3><a name = blastp><FONT color="green">
+         BLASTP Program Advanced Options</FONT></a></h3>
+    <h3><a name = blastx><FONT color="green">
+        BLASTX Program Advanced Options</FONT></a></h3>
+    <h3><a name = tblastn><FONT color="green">
+        TBLASTN Program Advanced Options</FONT></a></h3>
+<PRE>
+  -G  Cost to open a gap [Integer]
+    default = 11
+  -E  Cost to extend a gap [Integer]
+    default = 1
+  -e  Expectation value (E) [Real]
+    default = 10.0
+  -W  Word size, default is 11 for blastn, 3 for other programs.
+  -v  Number of one-line descriptions (V) [Integer]
+    default = 100
+  -b  Number of alignments to show (B) [Integer]
+    default = 100
+
+
+  Limited values for gap existence and extension are supported for these three programs.  
+  Some supported and suggested values are:
+
+  Existence	Extension
+
+     10             1
+     10             2
+     11             1
+      8             2
+      9             2
+     
+</PRE>
+<HR>
+
+    <!-- Created: Mon Jun 16 12:38:19 EDT 1997 -->
+<!-- hhmts start -->
+Last modified: Mon July 31, 1997
+<!-- hhmts end -->
+<BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR>
+<BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR><BR>
+
+  </body>
+</html>
diff --git a/network/wwwblast/docs/matrix_info.html b/network/wwwblast/docs/matrix_info.html
new file mode 100644
index 00000000..55dde5ae
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+++ b/network/wwwblast/docs/matrix_info.html
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+<html>
+<head>
+	<title> Matrix and Gap Costs </title>
+</head>
+<body bgcolor = "white">
+
+	
+
+<h3> <a name = matrix>Matrix</a> </h3>
+
+<P>
+  A key element in evaluating the quality of a pairwise sequence alignment
+is the "substitution matrix", which assigns a score for aligning any possible
+pair of residues.  The theory of amino acid substitution matrices is described
+in [1], and applied to DNA sequence comparison in [2].  In general, different
+substitution matrices are tailored to detecting similarities among sequences
+that are diverged by differing degrees [1-3].  A single matrix may nevertheless
+be reasonably efficient over a relatively broad range of evolutionary change
+[1-3].  Experimentation has shown that the BLOSUM-62 matrix [4] is among the
+best for detecting most weak protein similarities.  For particularly long
+and weak alignments, the BLOSUM-45 matrix may prove superior.  A detailed
+statistical theory for gapped alignments has not been developed, and the best
+<a href = "#open">gap costs</a> to use with a given substitution matrix are determined empirically.
+  Short alignments need to be relatively strong (i.e. have a higher percentage
+of matching residues) to rise above background noise.  Such short but strong
+alignments are more easily detected using a matrix with a higher "relative
+entropy" [1] than that of BLOSUM-62.  In particular, short query sequences
+can only produce short alignments, and therefore database searches with
+short queries should use an appropriately tailored matrix.  The BLOSUM series
+does not include any matrices with relative entropies suitable for the shortest
+queries, so the older PAM matrices [5,6] may be used instead.  For proteins,
+a provisional table of recommended substitution matrices and gap costs for
+various query lengths is:
+
+<PRE>
+     Query length     Substitution matrix     Gap costs
+     ------------     -------------------     ---------
+     <35              PAM-30                  ( 9,1)
+     35-50            PAM-70                  (10,1)
+     50-85            BLOSUM-80               (10,1)
+     >85              BLOSUM-62               (11,1)
+
+</PRE>
+
+<a name = extended></a>
+<h3> <a name = open>Gap Costs </a></h3>
+
+<P>
+  The raw score of an alignment is the sum of the scores for aligning pairs of
+residues and the scores for gaps.  Gapped BLAST and PSI-BLAST use "affine gap
+costs" which charge the score -a for the existence of a gap, and the score -b
+for each residue in the gap.  Thus a gap of k residues receives a total score
+of -(a+bk); specifically, a gap of length 1 receives the score -(a+b).
+
+<h3> <a name = lambda>Lambda Ratio </a></h3>
+
+<P>
+  To convert a raw score S into a normalized score S' expressed in bits,
+one uses the formula S' = (lambda*S - ln K)/(ln 2), where lambda and K are
+parameters dependent upon the scoring system (substitution matrix and gap
+costs) employed [7-9].  For determining S', the more important of these
+parameters is lambda.  The "lambda ratio" quoted here is the ratio of the
+lambda for the given scoring system to that for one using the same substitution
+scores, but with infinite gap costs [8].  This ratio indicates what proportion
+of information in an ungapped alignment must be sacrificed in the hope of
+improving its score through extension using gaps.  We have found empirically
+that the most effective gap costs tend to be those with lambda ratios in the
+range 0.8 to 0.9.
+
+<PRE>
+<A HREF="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=91269329&form=6&db=m&Dopt=r">[1]</A> Altschul, S.F. (1991) "Amino acid substitution matrices from an information
+    theoretic perspective." J. Mol. Biol. 219:555-565.
+[2] States, D.J., Gish, W. & Altschul, S.F. (1991) "Improved sensitivity of
+    nucleic acid database searches using application-specific scoring matrices."
+    Methods 3:66-70.
+<A HREF="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=93247069&form=6&db=m&Dopt=r">[3]</A> Altschul, S.F. (1993) "A protein alignment scoring system sensitive at all
+    evolutionary distances." J. Mol. Evol. 36:290-300.
+<A HREF="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=93066354&form=6&db=m&Dopt=r">[4]</A> Henikoff, S. & Henikoff, J.G. (1992) "Amino acid substitution matrices from
+    protein blocks." Proc. Natl. Acad. Sci. USA 89:10915-10919.
+[5] Dayhoff, M.O., Schwartz, R.M. & Orcutt, B.C. (1978) "A model of evolutionary
+    change in proteins." In "Atlas of Protein Sequence and Structure, vol. 5,
+    suppl. 3," M.O. Dayhoff (ed.), pp. 345-352, Natl. Biomed. Res. Found.,
+    Washington, DC.
+[6] Schwartz, R.M. & Dayhoff, M.O. (1978) "Matrices for detecting distant
+    relationships." In "Atlas of Protein Sequence and Structure, vol. 5,
+    suppl. 3," M.O. Dayhoff (ed.), pp. 353-358, Natl. Biomed. Res. Found.,
+    Washington, DC.
+<A HREF="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=90192788&form=6&db=m&Dopt=r">[7]</A> Karlin, S. & Altschul, S.F. (1990) "Methods for assessing the statistical
+    significance of molecular sequence features by using general scoring
+    schemes." Proc. Natl. Acad. Sci. USA 87:2264-2268.
+<A HREF="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8743700&form=6&db=m&Dopt=r">[8]</A> Altschul, S.F. & Gish, W. (1996) "Local alignment statistics." Meth.
+    Enzymol. 266:460-480.**
+<A HREF="http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r">[9]</A> Altschul, S.F., Madden, T.L., Sch&auml;ffer, A.A., Zhang, J., Zhang, Z., Miller,
+    W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of
+    protein database search programs." Nucleic Acids Res. 25:3389-3402.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+</PRE>
+</BODY>
+</HTML>
+
diff --git a/network/wwwblast/docs/megablast_readme.html b/network/wwwblast/docs/megablast_readme.html
new file mode 100644
index 00000000..696bd2d8
--- /dev/null
+++ b/network/wwwblast/docs/megablast_readme.html
@@ -0,0 +1,33 @@
+<head>
+<TITLE>MEGABLAST</TITLE>
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >
+<!-- Changed by: Sergei Shavirin,  9-May-1996 -->
+</head>
+
+<h1 align = center>MEGABLAST Search</h1>
+
+Mega BLAST uses the greedy algorithm for nucleotide sequence alignment search. This program is optimized for aligning sequences that differ slightly as a result of sequencing or other similar "errors". When larger word size is used (see explanation below), it is up to 10 times faster than more common sequence similarity programs. Mega BLAST is also able to efficiently handle much longer DNA sequences than the blastn program of traditional BLAST algorithm. 
+
+<center><h2> Parameters </h2></center>
+<h3><a name="wordsize"></a>Word size</h3> 
+Word size is roughly the minimal length of an identical match an alignment must contain if it is to be found by the algorithm. Mega BLAST is most efficient with word sizes 16 and larger, although word size as low as 8 can be used. <BR>
+If the value W of the word size is divisible by 4, it guarantees that all perfect matches of length W + 3 will be found and extended by Mega BLAST search, however perfect matches of length as low as W might also be found, although the latter is not guaranteed. Any value of W not divisible by 4 is equivalent to the nearest value divisible by 4 (with 4i+2 equivalent to 4i).
+
+<h3><a name="percident"></a>Percent identity</h3>
+If this parameter P is set, only the alignments with identity percentage higher than P will be retained. Also the default match reward and mismatch penalty scores are chosen in this case close to the log-odds (i.e. the most statistically effective) scores for the PAM distance corresponding to a sequence conservation level somewhat higher than P. The following table shows the relation between the percent identity cut-off values, the target conservation levels and the corresponding log-odds match and mismatch scores used by Mega BLAST:
+<table><tr>
+<td>Percent<br>Identity</td><td>Target</td><td>Match<br>score</td><td>Mismatch<br>score</td>
+</tr>
+<tr><td>None</td><td>95</td><td>1</td><td>-2</td></tr>
+<tr><td>&gt= 95</td><td>99</td><td>1</td><td>-3</td></tr>
+<tr><td>85, 90</td><td>95</td><td>1</td><td>-2</td></tr>
+<tr><td>80</td><td>88</td><td>2</td><td>-3</td></tr>
+<tr><td>75</td><td>83</td><td>4</td><td>-5</td></tr>
+</table>
+
+<h3><a name="gapping"></a>Gapping parameters</h3>
+By default, non-affine gapping parameters are assumed. This means that the gap opening penalty is 0, and gap extension penalty E can be computed from match reward r and mismatch penalty q by the formula: E = r/2 - q. The non-affine version of Mega BLAST requires significantly less memory and is also significantly faster, however affine gapping parameters can also be used, preferably with larger word sizes. Non-affine gapping parameters tend to yield alignments with more gaps, but the gap lengths are shorter.
+
+<h3><a name="xdropoff"></a>X-dropoff value</h3>
+As in BLAST, this value provides a cutoff threshold for the extension algorithm tree exploration. When the score of a given branch drops below the current best score minus the X-dropoff, the exploration of this branch stops. However the actual values of the X-dropoff for Mega BLAST and for traditional nucleotide BLAST algorithms are not necessarily compatible, i.e. with the same word size, match, mismatch and gapping penalties and with the same X-dropoff, the two algorithms might produce different results, which can be remedied by changing the X-dropoff value for one of the algorithms.
+
diff --git a/network/wwwblast/docs/newoptions.html b/network/wwwblast/docs/newoptions.html
new file mode 100644
index 00000000..e0b55bae
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+++ b/network/wwwblast/docs/newoptions.html
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+<TITLE>BLAST search main parameters</TITLE>
+<!-- Changed by: Sergei Shavirin,  2-Apr-1996 -->
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >  
+<h1>BLAST Search main parameters</h1>
+<HR>
+<p>
+<dl>
+<dt><b><a name = descriptions>DESCRIPTIONS</a></b>
+<dd>Restricts the number of short descriptions of matching
+sequences reported to the number specified; default
+limit is 100 descriptions.  See also EXPECT.
+<dt><b><a name = alignments>ALIGNMENTS</a></b>
+<dd>Restricts database sequences to the number specified for
+which high-scoring segment pairs (HSPs) are reported;
+the default limit is 100.  If more database sequences
+than this happen to satisfy the statistical
+significance threshold for reporting (see EXPECT below), 
+only the matches ascribed the greatest statistical 
+significance are reported.
+<dt><b><a name = expect>EXPECT</a></b>
+<dd>
+The statistical significance threshold for reporting
+matches against database sequences; the default value
+is 10, such that 10 matches are expected to be found
+merely by chance, according to the stochastic model
+of Karlin and Altschul (1990).  If the statistical
+significance ascribed to a match is greater than the
+EXPECT threshold, the match will not be reported.
+Lower EXPECT thresholds are more stringent, leading
+to fewer chance matches being reported.  Fractional
+values are acceptable.
+<dt><b><a name = inclusion>INCLUSION THRESHOLD</a></b>
+<dd>
+The statistical significance threshold for including a sequence
+in the model used by PSI-BLAST on the next iteration.
+<dt><b><a name = organism>ORGANISM NAME</a></b>
+<dd>
+Enter the organism name in the form "Genus species" (e.g., "Homo sapiens").
+A number of popular organism names are listed on a pull-down menu.
+
+<dt><b><a name = taxonomic>TAXONOMIC CLASSIFICATION</a></b>
+<dd>
+Enter any taxonomic group from the NCBI taxonomy (e.g. "Mammalia").
+
+<PRE>
+Some popular groups are:
+
+Archaea
+Bacteria
+Eukaryota
+Embryophyta (higher plants)
+Fungi
+Metazoa	(multicellular animals)
+Vertebrata
+Mammalia
+Rodentia
+Primates
+</PRE>
+
+<P>
+<A HREF="/Taxonomy/tax.html">Explore the taxonomy database at NCBI</A>
+
+<dt><b><a name = filter>FILTER (Low-complexity)</a></b>
+<dd> 
+Mask off segments of the query sequence that have
+low compositional complexity, as determined by the
+SEG program of Wootton & Federhen (Computers and
+Chemistry, 1993) or, for BLASTN, by the DUST
+program of Tatusov and Lipman (in preparation).  
+Filtering can eliminate statistically significant but 
+biologically uninteresting reports from the blast 
+output (e.g., hits against common acidic-, basic- or 
+proline-rich regions), leaving the more biologically 
+interesting regions of the query sequence available 
+for specific matching against database sequences. <BR>
+
+Filtering is only applied to the query sequence (or
+its translation products), not to database sequences.
+Default filtering is DUST for BLASTN, SEG for other
+programs. <BR>	
+
+It is not unusual for nothing at all to be masked
+by SEG, when applied to sequences in SWISS-PROT, 
+so filtering should not be expected to
+always yield an effect.  Furthermore, in some cases,
+sequences are masked in their entirety, indicating that
+the statistical significance of any matches reported
+against the unfiltered query sequence should be suspect.
+
+<dt><b><a name = filter>FILTER (Human repeats)</a></b>
+<dd> 
+
+This option masks Human repeats (LINE's and SINE's) and is especially
+useful for human sequences that may contain these repeats.  This
+option is still experimental and under development, so it 
+may change in the near future.<BR>
+ 
+<dt><b><a name = filter>FILTER (Mask for lookup table only)</a></b>
+<dd> 
+
+This option masks only for purposes of constructing the lookup
+table used by BLAST.  The BLAST extensions are performed without
+masking.  This option is still experimental and may change in the
+near future.
+
+
+<dt><b><a name = ncbi-gi>NCBI-gi<a></b>
+<dd> 
+Causes NCBI gi identifiers to be shown in the output,
+in addition to the accession and/or locus name.	
+
+<dt><b><a name = gencodes>Query Genetic Code<a></b>
+<dd> 
+Genetic code to be used in blastx translation of the query.
+
+<dt><b><a name = graphical-overview>Graphical Overview<a></b>
+<dd> 
+An overview of the database sequences aligned to the query 
+sequence is shown.  The score of each alignment is indicated
+by one of five different colors, which divides the range
+of scores into five groups.  Multiple alignments on the
+same database sequence are connected by a striped line.  
+<FONT color=red>Mousing over</FONT> a hit sequence 
+causes the definition and score to be shown in the
+window at the top, <FONT color=red>clicking</FONT> on a hit sequence takes the user to 
+the associated alignments.
+
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+
+
+
+
diff --git a/network/wwwblast/docs/oof_notation.html b/network/wwwblast/docs/oof_notation.html
new file mode 100644
index 00000000..70a78e43
--- /dev/null
+++ b/network/wwwblast/docs/oof_notation.html
@@ -0,0 +1,121 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<HTML>
+  <HEAD>
+    <title>Out-of-frame notation</title>
+  </HEAD>
+
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >
+<HR>
+<H1><CENTER>Out-Of-Frame BLAST notation</CENTER></H1>
+<HR>
+When protein aligned to the nucleotide there are 6 possibilities of
+match at any point. In OOF alignment - upper sequence is DNAP - 3-frame 
+translated DNA. Lower sequence is protein. At any position next protein 
+base may be aligned to 6 possible bases in DNAP:
+<P>
+(TBO - traditional blast output)
+<P>
+0:  &nbsp; &nbsp; &nbsp; &nbsp; 3 nucleotides missing - gap (TBO notation "-")
+<PRE>
+
+OOF alignment with DNAP:
+
+      DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGG-GVLCV
+      |  |  |  |  |  |  |  |  |  |  |  |  |  |  |   |  |
+      D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  G K V  V
+
+TBO:
+
+      DGTKFATGGQGQDSG-VV
+      DGTKFATGGQGQDSG VV
+      DGTKFATGGQGQDSGKVV
+
+</PRE>
+1: &nbsp; &nbsp; &nbsp; &nbsp; 2 nucleotides missing - "frameshift -2" (TBO notation "\\")
+<PRE>
+
+OOF alignment with DNAP:
+
+      DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGGGVLCV
+      |  |  |  |  |  |  |  |  |  |  |  |  |  |  |/  |  |
+      D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  GK  V  V
+
+TBO:
+
+      DGTKFATGGQGQDSG\\GVV
+      DGTKFATGGQGQDSG   VV
+      DGTKFATGGQGQDSG  KVV
+
+</PRE>
+2:  &nbsp; &nbsp; &nbsp; &nbsp; 1 nucletide missing - "frameshift -1" (TBO notation "\")
+<PRE>
+
+OOF alignment with DNAP:
+
+      DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGERGV
+      |  |  |  |  |  |  |  |  |  |  |  |  |  | /  |  |  
+      D  G  T  K  F  A  T  G  G  Q  G  Q  D  S G  K  V  
+TBO:
+
+      DGTKFATGGQGQDS\GEV
+      DGTKFATGGQGQDS G V
+      DGTKFATGGQGQDS GKV  
+
+</PRE>
+3:  &nbsp; &nbsp; &nbsp; &nbsp; Complete match
+<PRE>
+
+OOF alignment with DNAP:
+
+      DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGEKRGV
+      |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 
+      D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  G  K  V 
+
+TBO:
+
+      DGTKFATGGQGQDSGKV
+      DGTKFATGGQGQDSGKV 
+      DGTKFATGGQGQDSGKV 
+
+</PRE>
+4:  &nbsp; &nbsp; &nbsp; &nbsp; 1 nucleotide insertion - "frameshift +1" (TBO notation "/")
+<PRE>
+
+OOF alignment with DNAP:
+
+      DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGVEKRGV
+      |  |  |  |  |  |  |  |  |  |  |  |  |  |  |   \
+      D  G  T  K  F  A  T  G  G  Q  G  Q  D  S  G   K  V
+
+TBO:
+
+      DGTKFATGGQGQDSG/KV
+      DGTKFATGGQGQDSG KV
+      DGTKFATGGQGQDSG KV
+
+</PRE>
+5:  &nbsp; &nbsp; &nbsp; &nbsp; 2 nucleotides insertion - "frameshift +2" (TBP notation "//")
+<PRE>
+
+OOF alignment with DNAP:
+
+      DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLFLWGGEKRGV
+      |  |  |  |  |  |  |  |  |  |  |  |  |  |    \  |  |
+      D  G  T  K  F  A  T  G  G  Q  G  Q  D  S    G  K  V
+
+TBO:
+
+      DGTKFATGGQGQDS//GKV
+      DGTKFATGGQGQDS  GKV
+      DGTKFATGGQGQDS  GKV
+
+</PRE>
+
+<HR>
+    <address><a href="mailto:shavirin@ncbi.nlm.nih.gov">Sergei Shavirin</a></address>
+<!-- Created: Tue Oct 17 10:07:24 EDT 2000 -->
+<!-- hhmts start -->
+Last modified: Tue Oct 17 10:56:56 EDT 2000
+<!-- hhmts end -->
+  </BODY>
+</HTML>
diff --git a/network/wwwblast/docs/options.html b/network/wwwblast/docs/options.html
new file mode 100644
index 00000000..2b341af2
--- /dev/null
+++ b/network/wwwblast/docs/options.html
@@ -0,0 +1,123 @@
+<TITLE>BLAST search main parameters</TITLE>
+<!-- Changed by: Sergei Shavirin,  2-Apr-1996 -->
+<BODY bgcolor="FFFFFF" link="0000FF" vlink="ff0000" text="000000" >  
+<h1>BLAST Search main parameters</h1>
+<HR>
+<p>
+<dl>
+<dt><b><a name = histogram>HISTOGRAM</a></b>
+<dd>Display a histogram of scores for each search; default
+is yes. (See parameter H in the BLAST Manual).
+<dt><b><a name = descriptions>DESCRIPTIONS</a></b>
+<dd>Restricts the number of short descriptions of matching
+sequences reported to the number specified; default
+limit is 100 descriptions.  (See parameter V in the
+manual page).  See also EXPECT and CUTOFF.
+<dt><b><a name = alignments>ALIGNMENTS</a></b>
+<dd>Restricts database sequences to the number specified for
+which high-scoring segment pairs (HSPs) are reported;
+the default limit is 50.  If more database sequences
+than this happen to satisfy the statistical
+significance threshold for reporting (see EXPECT and
+CUTOFF below), only the matches ascribed the greatest
+statistical significance are reported.
+(See parameter B in the BLAST Manual).
+<dt><b><a name = expect>EXPECT</a></b>
+<dd>
+The statistical significance threshold for reporting
+matches against database sequences; the default value
+is 10, such that 10 matches are expected to be found
+merely by chance, according to the stochastic model
+of Karlin and Altschul (1990).  If the statistical
+significance ascribed to a match is greater than the
+EXPECT threshold, the match will not be reported.
+Lower EXPECT thresholds are more stringent, leading
+to fewer chance matches being reported.  Fractional
+values are acceptable.  (See parameter E in the BLAST
+Manual).
+<dt><b><a name = cutoff>CUTOFF</a></b>
+<dd>        
+Cutoff score for reporting high-scoring segment pairs.
+The default value is calculated from the EXPECT value
+(see above).  HSPs are reported for a database sequence
+only if the statistical significance ascribed to them
+is at least as high as would be ascribed to a lone
+HSP having a score equal to the CUTOFF value.  Higher
+CUTOFF values are more stringent, leading to fewer
+chance matches being reported.  (See parameter S in
+the BLAST Manual).  Typically, significance thresholds
+can be more intuitively managed using EXPECT.
+<dt><b><a name = matrix>MATRIX</a></b>
+<dd> 
+Specify an alternate scoring matrix for BLASTP, BLASTX,
+TBLASTN and TBLASTX.  The default matrix is BLOSUM62
+(Henikoff & Henikoff, 1992).  The valid alternative
+choices include:  PAM40, PAM120, PAM250 and IDENTITY.
+No alternate scoring matrices are available for BLASTN;
+specifying the MATRIX directive in BLASTN requests
+returns an error response.
+<dt><b><a name = strand>STRAND</a></b>
+<dd> 
+Restrict a TBLASTN search to just the top or bottom
+strand of the database sequences; or restrict a BLASTN,
+BLASTX or TBLASTX search to just reading frames on the
+top or bottom strand of the query sequence.
+<dt><b><a name = filter>FILTER</a></b>
+<dd> 
+Mask off segments of the query sequence that have
+low compositional complexity, as determined by the
+SEG program of Wootton & Federhen (Computers and
+Chemistry, 1993), or segments consisting of
+short-periodicity internal repeats, as determined
+by the XNU program of Claverie & States (Computers
+and Chemistry, 1993), or, for BLASTN, by the DUST
+ program of Tatusov and Lipman (in preparation).  
+Filtering can eliminate statistically significant but 
+biologically uninteresting reports from the blast 
+output (e.g., hits against common acidic-, basic- or 
+proline-rich regions), leaving the more biologically 
+interesting regions of the query sequence available 
+for specific matching against database sequences. <BR>
+
+Filtering is only applied to the query sequence (or
+its translation products), not to database sequences.
+Default filtering is DUST for BLASTN, SEG for other
+programs. <BR>	
+
+It is not unusual for nothing at all to be masked
+by SEG, XNU, or both, when applied to sequences
+in SWISS-PROT, so filtering should not be expected to
+always yield an effect.  Furthermore, in some cases,
+sequences are masked in their entirety, indicating that
+the statistical significance of any matches reported
+against the unfiltered query sequence should be suspect.
+
+<dt><b><a name = ncbi-gi>NCBI-gi<a></b>
+<dd> 
+Causes NCBI gi identifiers to be shown in the output,
+in addition to the accession and/or locus name.	
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+<BR>
+
+
+
+
diff --git a/network/wwwblast/docs/pattern.html b/network/wwwblast/docs/pattern.html
new file mode 100644
index 00000000..a250a487
--- /dev/null
+++ b/network/wwwblast/docs/pattern.html
@@ -0,0 +1,139 @@
+<HTML>
+<TITLE>PHI Blast Pattern description</TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<h2>Rules for pattern syntax for PHI-BLAST.</h2>
+
+The syntax for patterns in PHI-BLAST follows the conventions
+of PROSITE. When using the stand-alone program, it
+is permissible to have multiple patterns in a file separated
+by a blank line between patterns. When using the Web-page
+only one pattern is allowed per query.
+<P>
+Valid protein characters for PHI-BLAST patterns:
+<PRE>
+    ABCDEFGHIKLMNPQRSTVWXYZU
+</PRE>
+Valid DNA characters for PHI-BLAST patterns:
+<PRE>
+    ACGT
+</PRE>
+Other useful delimiters:
+<PRE>
+    [ ]    means any one of the characters enclosed in the brackets
+        e.g., [LFYT] means one occurrence of L or F or Y or T
+    -      means nothing (this is a spacer character used by PROSITE)
+    x with nothing following means any residue
+    x(5)  means 5 positions in which any residue is allowed (and similarly for any other
+          single number in parentheses after x)
+    x(2,4) means 2 to 4 positions where any residue is allowed,
+           and similarly for any other two numbers separated by a comma;
+           the first number should be < the second number.           
+    >      can occur only at the end of a pattern and means nothing
+           it may occur before a period
+           (another spacer used by PROSITE)
+
+    .      may be used at the end of the pattern and means nothing
+</PRE>
+When using the stand-alone program, the pattern should
+be in a file, with the first line starting:
+<PRE>
+ ID
+</PRE>
+followed by 2 spaces and a text string givign the pattern a name.
+<P>
+There should also be a line starting
+<PRE>
+ PA
+</PRE>
+followed by 2 spaces followed by the pattern description.
+<P>
+All other PROSITE codes in the first two columns are allowed,
+but only the HI code, described below is relevant to PHI-BLAST.
+<P>
+Here is an example from PROSITE.
+<PRE>
+ID   CNMP_BINDING_2; PATTERN.
+AC   PS00889;
+DT   OCT-1993 (CREATED); OCT-1993 (DATA UPDATE); NOV-1995 (INFO UPDATE).
+DE   Cyclic nucleotide-binding domain signature 2.
+PA   [LIVMF]-G-E-x-[GAS]-[LIVM]-x(5,11)-R-[STAQ]-A-x-[LIVMA]-x-[STACV].
+NR   /RELEASE=32,49340;
+NR   /TOTAL=57(36); /POSITIVE=57(36); /UNKNOWN=0(0); /FALSE_POS=0(0);
+NR   /FALSE_NEG=1; /PARTIAL=1;
+CC   /TAXO-RANGE=??EP?; /MAX-REPEAT=2;
+</PRE>
+The line starting
+<PRE>
+    ID
+</PRE>
+gives the pattern a name.
+The lines starting
+<PRE>
+     AC, DT, DE, NR, NR, CC
+</PRE>
+are relevant to PROSITE users, but irrelevant to PHI-BLAST.
+These lines are tolerated, but ignored by PHI-BLAST.
+<P>
+The line starting
+<PRE>
+     PA
+describes the pattern as:
+      one of LIVMF
+followed by
+      G
+followed by
+      E
+followed by 
+      any single character
+followed by
+      one of GAS
+followed by
+      one of LIVM
+followed by 
+      any 5 to 11 characters
+followed by
+      R
+followed by
+      one of STAQ
+followed by
+      A
+followed by
+      any single character
+followed by
+      one of LIVMA
+followed by
+      any single character
+followed by 
+      one of STACV
+</PRE>
+In this case the pattern ends with a period.
+It can end with nothing after the last specifying symbol
+or any number of > signs or periods or combination thereof.
+<P>
+Here is another example, illustrating the use of an HI line.
+<PRE>
+ID    ER_TARGET; PATTERN.
+PA  [KRHQSA]-[DENQ]-E-L>.
+HI (19 22)
+HI (201 204)
+</PRE>
+In this example, the HI lines specify that the pattern
+occurs twice, once from positions 19 through 22 in the
+sequence and once from positions 201 through 204 in the
+sequence.
+These specifications are relevant when stand-alone PHI-BLAST is
+used with the "seedp"
+option, in which the interesting occurrences of the pattern
+in the sequence are specified. In this case the
+HI lines specify which occurrence(s) of the pattern
+should be used to find good alignments.
+<P>
+In general, the seedp option is more useful than the
+standard patternp option ONLY when the
+pattern occurs K > 1 times in the sequence AND
+the user is interested in matching to J < K of those
+occurrences.
+Then using the HI lines enables the user to specify which
+occurrences are of interest.
+</BODY>
+</HTML>
diff --git a/network/wwwblast/docs/taxblasthelp.html b/network/wwwblast/docs/taxblasthelp.html
new file mode 100644
index 00000000..2d52db9d
--- /dev/null
+++ b/network/wwwblast/docs/taxblasthelp.html
@@ -0,0 +1,178 @@
+<HTML>
+    <TITLE>Tax BLAST Help</TITLE>
+    <HEAD>
+      <META http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+      <META NAME="keywords" CONTENT="taxonomy,organizm,BLAST">
+      <META NAME="description" CONTENT="Taxonomy BLAST description.">
+      <LINK REL="stylesheet" href="http://www.ncbi.nlm.nih.gov/corehtml/ncbi_test.css">
+    </HEAD>
+  <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+
+    <table border="0" width="100%" cellspacing="0" cellpadding="0">
+      <tr> 
+        <td width="140"><a href="http://www.ncbi.nlm.nih.gov"> <img src="http://www.ncbi.nlm.nih.gov/corehtml/left.GIF" width="130" height="45" border="0"></a></td>
+        <td valign="BOTTOM"><img src="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/html/taxonomylogo.gif" alt="Taxonomy Logo" border=0></td>
+      </tr>
+    </table>
+    <!--  the quicklinks bar   --> 
+    <table CLASS="TEXT" border="0" width="100%" cellspacing="0" cellpadding="3" bgcolor="#000000" fgcolor="#FFFFFF">
+      <tr CLASS="TEXT"  align="CENTER"> 
+        <td width=100><a href="http://www.ncbi.nlm.nih.gov/PubMed/" class="BAR">PubMed</a></td>
+        <td width=100><a href="http://www.ncbi.nlm.nih.gov/Entrez/" class="BAR">Entrez</a></td>
+        <td width=100><a href="http://www.ncbi.nlm.nih.gov/BLAST/" class="BAR">BLAST</a></td>
+        <td width=100><a href="http://www.ncbi.nlm.nih.gov/omim/" class="BAR">OMIM</a></td>
+        <td width=100><a href="/Taxonomy/taxonomyhome.html"  class="BAR">Taxonomy</a></td>
+        <td width=100><a href="http://www.ncbi.nlm.nih.gov/Structure/" class="BAR">Structure</a></td>
+      </tr>
+    </table>
+    
+<CENTER><H2>Taxonomy BLAST Help</H2></CENTER>
+<HR>
+The BLAST Taxonomy Reports page (Tax BLAST) presents three different 
+views of the results of a given BLAST run, based on the information in 
+<a href="http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html">the NCBI Taxonomy Database.</a> The Tax BLAST reports only include the organisms that 
+are found in the BLAST hitlist.
+
+<h3>Organism Report</h3>
+
+The simplest report is 'Organism Report'.
+<P>
+This report sorts the BLAST hits according to the species of the target 
+sequence, so that all of the hits to the same organism will appear 
+together. Within each species, the BLAST hits are sorted by score 
+(as for the normal BLAST output). The species themselves are sorted
+by the strength of their strongest BLAST hit scores.
+<P>
+Each organism entry in the organism report contains a header line
+with up to four pieces of information:
+<PRE>
+  Bombyx mori (domestic silkworm) [moths] taxid 7091
+  ^^^^^^^^^^^  ^^^^^^^^^^^^^^^^^   ^^^^^  ^^^^^^^^^^
+      1                2             3         4
+</PRE>
+    <OL>
+      <LI>the scientific name of the organism
+      <LI>a vernacular (common) name for the organism, if one is available
+      <LI>the 'blast name' 
+      <LI>the 'taxid'
+    </OL>
+The 'blast name' is a common name for a large group of organisms
+(e.g. 'mammals' 'flatworms' or 'fungi') that is intended to give a
+general idea of what kind of organism this is, when the scientific
+name is not familiar.
+<P>
+The 'taxid' is the stable unique identifier for this organism
+in the NCBI taxonomy database.
+<P>
+<b><i>note:</i></b> Some sequence entries may be annotated with names classified
+below the species level - these will be treated separately in the
+Tax BLAST reports. For example, there may be entries for both
+"Homo sapiens" and for "Homo sapiens neandertalensis".
+<P>
+<b><i>note:</i></b> If two sequence entries from different species are identical
+(e.g. EF-1 alpha from human AAA18502 and rabbit CAA27245), only one
+of them will appear in the Tax BLAST reports.
+<P>
+<b><i>note:</i></b> Some sequence entries do not have source organism 
+information 
+(most patent entries, for example). These will be included in the 
+Tax BLAST reports under the heading "Unresolved taxid".
+
+<h3>Lineage Report</h3>
+
+The lineage report gives a simplified view of the relationships 
+between the organisms, according to their classification in the
+taxonomy database. This report is 'focused' on the organism which 
+yielded the strongest BLAST hit. Note that if the query sequence 
+itself was taken from the database, then the lineage report will 
+be focuses on the organism yielded the strongest BLAST hit.
+<P>
+The lineage report answers the question "how closely are the 
+organisms in the BLAST hitlist related to the query sequence
+(focus organism) according to the taxonomy database".
+<P>
+The top part of the report shows an abbreviated lineage down
+to the focus organism:
+<PRE>
+Fungi/Metazoa group [eukaryotes]
+. Eumetazoa           [animals]
+. . Bilateria           [animals]
+. . . Coelomata           [animals]
+. . . . Deuterostomia       [animals]
+. . . . . Euteleostomi        [vertebrates]
+. . . . . . Tetrapoda           [vertebrates]
+. . . . . . . Amniota             [vertebrates]
+. . . . . . . . Eutheria            [mammals]
+. . . . . . . . . Homo sapiens (human) ------------------- ...
+</PRE>
+This list includes the smallest subset of taxonomic groups
+that are required to represent the relationships between the
+BLAST hitlist organisms and the focus species. The nested vernacular 
+'blast names' on the right give a rough approximation of the
+relationships of each species. The first name in the list gives the 
+taxonomic range of the BLAST hitlist organisms - all of the species
+in this list come from the "Fungi/Metazoa group".
+<P>
+The bottom part of the lineage report has a left and a right side.
+The left side of the report lists the species names (with a common
+name, if one is available) nested as they appear within the
+taxonomic groups in the top part of the report. Within each
+nesting, the species are sorted by the strength of the strongest
+BLAST hit.
+<PRE>
+. . . . Deuterostomia       [animals]
+. . . . . Euteleostomi        [vertebrates]
+. . . . . . Tetrapoda           [vertebrates]
+. . . . . . . Amniota             [vertebrates]
+. . . . . . . . Eutheria            [mammals]
+. . . . . . . . . Homo sapiens (human) -------------------  941 ...
+. . . . . . . . . Cricetulus griseus (Chinese hamster) ...  939 ...
+. . . . . . . . . Mus musculus (house mouse) .............  939 ...
+. . . . . . . . . Rattus norvegicus (Norway rat) .........  936 ...
+. . . . . . . . Gallus gallus (chicken) ------------------  938 ...
+. . . . . . . Xenopus laevis (African clawed frog) -------  914 ...
+. . . . . . Danio rerio (zebrafish) ----------------------  872 ...
+. . . . . . Oryzias latipes (Japanese medaka) ............  833 ...
+. . . . . . Seriola quinqueradiata (five-ray yellowtail) .  823 ...
+. . . . . . Sparus aurata (gilthead sea bream) ...........  820 ...
+. . . . . Anthocidaris crassispina -----------------------  782 ...
+</PRE>
+This report focuses on Homo sapiens, the source of the best hit.
+Cricetulus griseus, Mus musculus and Rattus norvegicus are all
+placental mammals (Eutheria) along with Homo sapiens, but none 
+are more closely related to Homo sapiens than thay are to one another.
+The next most closely related species is the chicken (an amniote), 
+and so on.
+<P>
+The right half of the report gives the BLAST score of the 
+strongest hit from each species (and the title of the corresponding
+sequence entry) the number of hits, and the 'blast name' associated
+with each of the species.
+
+<h3>Taxonomy Report</h3>
+
+This report summarizes everything that our classification has 
+to say about the relationships between all of the organisms found
+in the BLAST hitlist. The left side of the report gives an
+abbreviated subset of our classification - only those taxonomic
+groups that are required to distinguish each of the organisms
+from all of the rest. The number of blast hits and the number
+of species in the hitlist are accumulated up each branch of the
+tree. This allows you to do a BLAST search with a Drosophila
+protein (for example) and to see how many hits were found in
+the Mammalia, or the Archaea, or any taxonomic group that is
+not in the Drosophila lineage.
+<P>
+The right side of the report fills in the rest of the lineage 
+(if any) that was not required in the abbreviated
+classification given on the left. This allows you to search
+using browser "Find" menu command for any of the taxonomic groups
+found in the lineage
+of any of the species in the blast hitlist set. This is often
+useful delete (for structural reasons) some very well-recognized
+taxa (e.g., Insecta and Mammalia) will not often appear in the
+abbreviated classifications found in these reports. 'Mammalia',
+for example will only appear in the abbreviated classification
+of these taxonomy reports if the BLAST hitlist includes 
+sequences from one of the monotremes (platypus or echidna)
+as well as a sequence from one of the other mammals.
diff --git a/network/wwwblast/images/0.gif b/network/wwwblast/images/0.gif
new file mode 100644
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+++ b/network/wwwblast/images/0.gif
diff --git a/network/wwwblast/images/00.gif b/network/wwwblast/images/00.gif
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+++ b/network/wwwblast/images/00.gif
diff --git a/network/wwwblast/images/1.gif b/network/wwwblast/images/1.gif
new file mode 100644
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diff --git a/network/wwwblast/images/2.gif b/network/wwwblast/images/2.gif
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+++ b/network/wwwblast/images/2.gif
diff --git a/network/wwwblast/images/3.gif b/network/wwwblast/images/3.gif
new file mode 100644
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+++ b/network/wwwblast/images/3.gif
diff --git a/network/wwwblast/images/L.gif b/network/wwwblast/images/L.gif
new file mode 100644
index 00000000..26d4fac0
--- /dev/null
+++ b/network/wwwblast/images/L.gif
diff --git a/network/wwwblast/images/U.gif b/network/wwwblast/images/U.gif
new file mode 100644
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+++ b/network/wwwblast/images/U.gif
diff --git a/network/wwwblast/images/bg.gif b/network/wwwblast/images/bg.gif
new file mode 100644
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+++ b/network/wwwblast/images/bg.gif
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+++ b/network/wwwblast/images/bl2seq.gif
diff --git a/network/wwwblast/images/blast_form.gif b/network/wwwblast/images/blast_form.gif
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+++ b/network/wwwblast/images/blast_form.gif
diff --git a/network/wwwblast/images/blast_results.gif b/network/wwwblast/images/blast_results.gif
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+++ b/network/wwwblast/images/blast_results.gif
diff --git a/network/wwwblast/images/checked.gif b/network/wwwblast/images/checked.gif
new file mode 100644
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+++ b/network/wwwblast/images/checked.gif
diff --git a/network/wwwblast/images/confused.gif b/network/wwwblast/images/confused.gif
new file mode 100644
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+++ b/network/wwwblast/images/confused.gif
diff --git a/network/wwwblast/images/megablast_form.gif b/network/wwwblast/images/megablast_form.gif
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diff --git a/network/wwwblast/images/new.gif b/network/wwwblast/images/new.gif
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+++ b/network/wwwblast/images/new.gif
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new file mode 100644
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+++ b/network/wwwblast/images/psi_blast.gif
diff --git a/network/wwwblast/images/rpsblast.gif b/network/wwwblast/images/rpsblast.gif
new file mode 100644
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diff --git a/network/wwwblast/index.html b/network/wwwblast/index.html
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@@ -0,0 +1,40 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<html>
+  <head>
+    <title>List of BLAST programs</title>
+  </head>
+
+<BODY LINK="#0000ff" VLINK="#800080" BGCOLOR="#ffffff" ALINK="#660099">
+<H2 ALIGN="CENTER">List of BLAST programs</h2>
+
+<UL>
+
+<LI> <A HREF=blast.html>Regular BLAST without client-server support</A>
+<LI> <A HREF=blast_cs.html>Regular BLAST with client-server support</A>
+
+<LI> <A HREF=psiblast.html>PSI/PHI BLAST without client-server support</A>
+<LI> <A HREF=psiblast_cs.html>PSI/PHI BLAST with client-server support</A>
+
+<LI> <A HREF=megablast.html>Mega BLAST without client-server support</A>
+<LI> <A HREF=megablast_cs.html>Mega BLAST with client-server support</A>
+
+<LI> <A HREF=rpsblast.html>RPS BLAST without client-server support</A>
+<LI> <A HREF=rpsblast_cs.html>RPS BLAST with client-server support</A>
+
+<LI> <A HREF=wblast2.html>BLAST 2 sequences without client-server support</A>
+<LI> <A HREF=wblast2_cs.html>BLAST 2 sequences with client-server support</A>
+
+<LI> <A HREF=readme.html>Readme file</A>
+
+</UL>
+
+
+
+    <hr>
+    <address><a href="mailto:blast-help@ncbi.nlm.nih.gov">BLAST Help Desk</a></address>
+<!-- Created: Wed May  2 11:56:07 EDT 2001 -->
+<!-- hhmts start -->
+Last modified: Wed May  2 12:06:28 EDT 2001
+<!-- hhmts end -->
+  </body>
+</html>
diff --git a/network/wwwblast/megablast.html b/network/wwwblast/megablast.html
new file mode 100644
index 00000000..2c9119a9
--- /dev/null
+++ b/network/wwwblast/megablast.html
@@ -0,0 +1,252 @@
+<!--
+/* $Id: megablast.html,v 1.4 2003/05/22 16:20:45 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: megablast.html,v $
+*
+* Author: Ilya Dondoshansky 
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.4 $
+*
+* File Description:
+*         Template for standalone Mega BLAST Web page
+*
+* $Log: megablast.html,v $
+* Revision 1.4  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.3  2003/05/05 18:14:02  dondosha
+* Uncommented discontiguous megablast options; added subsequence options
+*
+* Revision 1.2  2002/08/06 20:09:19  dondosha
+* Added commented out HTML code for discontiguous word options
+*
+* Revision 1.1  2002/08/06 19:03:51  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/megablast_form.gif" ISMAP> 
+
+<HEAD>
+<SCRIPT>
+function megablastDefaults(f, on, off) {
+   if (on && !off) {
+         f.UNGAPPED_ALIGNMENT.checked = off;
+   } 
+   if (off && (on || f.MEGABLAST.checked)) {
+      f.MEGABLAST.checked = !off;
+   }
+}
+</SCRIPT>
+</HEAD>
+
+<FORM ACTION="blast.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<B>Choose program to use and database to search:</B>
+<P>
+<a href="docs/blast_program.html">Program: BLASTN </a> &nbsp;
+<INPUT TYPE="checkbox" NAME="MEGABLAST" VALUE="is_set" CHECKED onClick="megablastDefaults(this.form,1,!checked);"> Use <a href="docs/megablast_readme.html">MegaBlast</a>
+<P>
+<a href="docs/blast_databases.html">Database</a>
+<select name = "DATALIB">
+    <option VALUE = "test_na_db"> test_na_db
+    <option VALUE = "test_aa_db"> test_aa_db
+</select>
+
+<!--
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+-->
+
+<P>
+Enter sequence below in <a href="docs/fasta.html">FASTA</a>  format 
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+<P>
+Set subsequence: From
+&nbsp;&nbsp<input TYPE="text" NAME="QUERY_FROM" VALUE="" SIZE="10">
+&nbsp;&nbsp&nbsp;&nbsp To
+<input TYPE="text" NAME="QUERY_TO" VALUE="" SIZE="10">
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value=
+'';MainBlastForm.QUERY_FROM.value='';MainBlastForm.QUERY_TO.value='';MainBlastForm
+.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+<HR>
+
+The query sequence is 
+<a href="docs/filtered.html">filtered</a> 
+for low complexity regions by default.
+<BR>
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+ <INPUT TYPE="checkbox" NAME="LCASE_MASK"> Mask lower case
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<INPUT TYPE="checkbox" NAME="UNGAPPED_ALIGNMENT" VALUE="is_set" onClick="megablastDefaults(this.form,0,checked);"> Perform ungapped alignment 
+<P>
+<a href="docs/megablast_readme.html">Word Size</a>
+<select name="WORD_SIZE">
+<option value="11">11</option>
+<option value="12">12</option>
+<option value="16">16</option>
+<option value="20">20</option>
+<option value="24">24</option>
+<option value="28" selected>28</option>
+<option value="32">32</option>
+<option value="48">48</option>
+<option value="64">64</option>
+</select>
+&nbsp;&nbsp;&nbsp;
+<a href="docs/megablast_readme.html" >Percent Identity</a>
+&nbsp;&nbsp;<select name="PERC_IDENT">
+<option value=0 selected>None</option>
+<option>99</option>
+<option>98</option>
+<option>95</option>
+<option>90</option>
+<option>85</option>
+<option>80</option>
+<option>75</option>
+<option>70</option>
+<option>60</option>
+</select>
+<P>
+<tr>
+<td align="right" valign="middle"><a href="docs/discontiguous.html">Discontiguous 
+Word options</a></font></td>
+<td align="left" nowrap valign="CENTER">&nbsp;&nbsp;<font size="-1">Template length
+ <select name="TEMPLATE_LENGTH">
+<option value=0 selected>Contiguous</option>
+<option>16</option>
+<option>18</option>
+<option>21</option>
+</select></font><font size="-1">Template type <select name="TEMPLATE_TYPE" size="0"
+><option selected value="0">Coding</option>
+<option value="1">Non-coding</option>
+<option value="2">Two templates</option>
+</select></font><font size="-1">Require 2 word hits for extension <input name="TWO_
+HITS" type="checkbox"></font></td>
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" MAXLENGTH="50">
+<HR>
+<!--
+<INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp;
+-->
+<INPUT TYPE="checkbox" NAME="OVERVIEW" CHECKED> 
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> query-anchored with identities
+    <option value=2> query-anchored without identities
+    <option value=3> flat query-anchored with identities
+    <option value=4> flat query-anchored without identities
+    <option value=7> BLAST XML
+    <option value=9> Hit Table
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option selected> 100 
+    <option> 250 
+    <option> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option selected> 50 
+    <option> 100 
+    <option> 250 
+    <option> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<a href="docs/megablast_readme.html">Return alignment endpoints only</a>&nbsp;&nbsp;
+<input name="ENDPOINTS" type="checkbox">
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/megablast_cs.html b/network/wwwblast/megablast_cs.html
new file mode 100644
index 00000000..323b7870
--- /dev/null
+++ b/network/wwwblast/megablast_cs.html
@@ -0,0 +1,251 @@
+<!--
+/* $Id: megablast_cs.html,v 1.4 2003/05/22 16:20:45 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: megablast_cs.html,v $
+*
+* Author: Ilya Dondoshansky 
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.4 $
+*
+* File Description:
+*         Template for standalone Mega BLAST Web page
+*
+* $Log: megablast_cs.html,v $
+* Revision 1.4  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.3  2003/05/05 18:14:02  dondosha
+* Uncommented discontiguous megablast options; added subsequence options
+*
+* Revision 1.2  2002/08/06 20:09:19  dondosha
+* Added commented out HTML code for discontiguous word options
+*
+* Revision 1.1  2002/08/06 19:03:51  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/megablast_form.gif" ISMAP> 
+
+<IMG SRC="images/megablast_form.gif" BORDER=0 ISMAP></A>
+
+<HEAD>
+<SCRIPT>
+function megablastDefaults(f, on, off) {
+   if (on && !off) {
+         f.UNGAPPED_ALIGNMENT.checked = off;
+   }
+   if (off && (on || f.MEGABLAST.checked)) {
+      f.MEGABLAST.checked = !off;
+   }
+}
+</SCRIPT>
+</HEAD>
+
+<FORM ACTION="blast_cs.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<B>Choose program to use and database to search:</B>
+<P>
+<a href="docs/blast_program.html">Program: BLASTN </a> &nbsp;
+<INPUT TYPE="checkbox" NAME="MEGABLAST" VALUE="is_set" CHECKED onClick="megablastDefaults(this.form,1,!checked);"> Use <a href="docs/megablast_readme.html">MegaBlast</a>
+<P>
+<a href="docs/blast_databases.html">Database</a>
+<select name = "DATALIB">
+    <option VALUE = "test_na_db"> test_na_db
+    <option VALUE = "test_aa_db"> test_aa_db
+</select>
+<P>
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+<INPUT TYPE="submit" VALUE="Search">&nbsp;&nbsp;
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.QUERY_FROM.value='';MainBlastForm.QUERY_TO.value='';MainBlastForm.SEQUENCE.focus();">
+
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+
+<P>Please read about <a href="/BLAST/fasta.html">FASTA</a> format description
+<P>
+Set subsequence: From
+&nbsp;&nbsp<input TYPE="text" NAME="QUERY_FROM" VALUE="" SIZE="10">
+&nbsp;&nbsp&nbsp;&nbsp To
+<input TYPE="text" NAME="QUERY_TO" VALUE="" SIZE="10">
+<P>
+<HR>
+
+The query sequence is 
+<a href="/BLAST/filtered.html">filtered</a> 
+for low complexity regions by default.
+<BR>
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+ <INPUT TYPE="checkbox" NAME="LCASE_MASK"> Mask lower case
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<INPUT TYPE="checkbox" NAME="UNGAPPED_ALIGNMENT" VALUE="is_set" onClick="megablastDefaults(this.form,0, checked);"> Perform ungapped alignment
+<P>
+<a href="docs/megablast_readme.html">Word Size</a>
+<select name="WORD_SIZE">
+<option value="11">12</option>
+<option value="12">12</option>
+<option value="16">16</option>
+<option value="20">20</option>
+<option value="24">24</option>
+<option value="28" selected>28</option>
+<option value="32">32</option>
+<option value="48">48</option>
+<option value="64">64</option>
+</select>
+&nbsp;&nbsp;&nbsp;
+<a href="docs/megablast_readme.html" >Percent Identity</a>
+&nbsp;&nbsp;<select name="PERC_IDENT">
+<option value=0 selected>None</option>
+<option>99</option>
+<option>98</option>
+<option>95</option>
+<option>90</option>
+<option>85</option>
+<option>80</option>
+<option>75</option>
+<option>70</option>
+<option>60</option>
+</select>
+<P>
+<tr>
+<td align="right" valign="middle"><a href="docs/discontiguous.html">Discontiguous 
+Word options</a></font></td>
+<td align="left" nowrap valign="CENTER">&nbsp;&nbsp;<font size="-1">Template length
+ <select name="TEMPLATE_LENGTH">
+<option value=0 selected>Contiguous</option>
+<option>16</option>
+<option>18</option>
+<option>21</option>
+</select></font><font size="-1">Template type <select name="TEMPLATE_TYPE" size="0"
+><option selected value="0">Coding</option>
+<option value="1">Non-coding</option>
+<option value="2">Two templates</option>
+</select></font><font size="-1">Require 2 word hits for extension <input name="TWO_
+HITS" type="checkbox"></font></td>
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" MAXLENGTH="50">&nbsp;
+<INPUT TYPE="checkbox" NAME="TAX_BLAST"> Show <a href ="docs/taxblasthelp.html">Tax Blast reports</a>
+<HR>
+
+<INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp;
+
+<INPUT TYPE="checkbox" NAME="OVERVIEW" CHECKED>
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> query-anchored with identities
+    <option value=2> query-anchored without identities
+    <option value=3> flat query-anchored with identities
+    <option value=4> flat query-anchored without identities
+    <option value=7> BLAST XML
+    <option value=9> Hit Table
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option selected> 100 
+    <option> 250 
+    <option> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option selected> 50 
+    <option> 100 
+    <option> 250 
+    <option> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<a href="docs/megablast_readme.html">Return alignment endpoints only</a>&nbsp;&nbsp;
+<input name="ENDPOINTS" type="checkbox">
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/ncbi_blast.rc b/network/wwwblast/ncbi_blast.rc
new file mode 100644
index 00000000..3ebba2e4
--- /dev/null
+++ b/network/wwwblast/ncbi_blast.rc
@@ -0,0 +1,28 @@
+# $Id: ncbi_blast.rc,v 1.1 2002/08/06 19:03:51 dondosha Exp $
+#
+#================================================================
+#
+#     This is dynamic configuration file for WWW BLAST service
+#              All lines started from '#' are ignored.
+#           "//" string considered as start of comments
+#
+#     Author Sergei B. Shavirin
+#
+# $Revision: 1.1 $
+#
+#
+##################################################################
+#
+#
+# Number of CPUs to use for a single request
+#
+NumCpuToUse     4
+#
+# Here are list of combinations program/database, 
+# that allowed by BLAST service. Format: <program> <db> <db> ...
+#
+blastn nr drosoph dbest est est_mouse est_human est_others kabat mito month dbsts sts vector pdb alu epd gss htgs ecoli yeast pat
+blastp nr drosoph kabat month swissprot pdb alu ecoli yeast pat mito
+blastx nr drosoph kabat month swissprot pdb alu ecoli yeast pat mito
+tblastn nr drosoph dbest est est_mouse est_human est_others kabat mito month dbsts sts vector pdb alu epd gss htgs ecoli yeast pat
+tblastx drosoph dbest est est_mouse est_human est_others kabat mito month dbsts sts vector pdb alu epd gss htgs ecoli yeast pat
diff --git a/network/wwwblast/psiblast.cgi b/network/wwwblast/psiblast.cgi
new file mode 100755
index 00000000..0875cec0
--- /dev/null
+++ b/network/wwwblast/psiblast.cgi
@@ -0,0 +1,14 @@
+#!/bin/csh -f
+
+#
+# $Id: psiblast.cgi,v 1.1 2002/08/06 19:03:51 dondosha Exp $
+#
+
+echo "Content-type: text/html"
+echo ""
+
+#setenv WWW_ROOT_PATH /blast
+#setenv DEBUG_COMMAND_LINE TRUE
+setenv BLASTDB db
+
+./psiblast.REAL
diff --git a/network/wwwblast/psiblast.html b/network/wwwblast/psiblast.html
new file mode 100644
index 00000000..cffe497f
--- /dev/null
+++ b/network/wwwblast/psiblast.html
@@ -0,0 +1,183 @@
+<!--
+/* $Id: psiblast.html,v 1.3 2003/06/24 21:53:54 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: psiblast.html,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.3 $
+*
+* File Description:
+*         Template for standalone PSI BLAST Web page
+*
+* $Log: psiblast.html,v $
+* Revision 1.3  2003/06/24 21:53:54  dondosha
+* Changed WWW_BLAST_TYPE to BLAST_TYPE
+*
+* Revision 1.2  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.1  2002/08/06 19:03:52  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/psi_blast.gif" ISMAP> 
+
+<FORM ACTION="psiblast.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<INPUT type="hidden" name = "BLAST_TYPE" value = "psiblast">
+<B>Choose <a href="docs/blast_databases.html">database</a> to use with PSI/PHI Blast:</B>&nbsp;&nbsp;
+<select name = "DATALIB">
+    <option VALUE = "test_aa_db"> test_aa_db
+    <option VALUE = "test_na_db"> test_na_db 
+</select>
+<input type="hidden" name = "PROGRAM" value="blastp">
+<P>
+Enter sequence below in <a href="docs/fasta.html">FASTA</a>  format 
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+<HR>
+
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER"> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+<P>
+<INPUT TYPE="checkbox" NAME="TWEAK_PARAMETERS" CHECKED> <a href ="docs/composition.html">Composition-based statistics</a> &nbsp; &nbsp; &nbsp; &nbsp;
+<INPUT TYPE="checkbox" NAME="SMITH_WATERMAN"> Compute Smith-Waterman alignments
+<P>
+<a href="docs/newoptions.html#alignments">Expect value for inclusion in PSI-BLAST iteration 1</a>
+<INPUT TYPE="text" NAME ="E_THRESH" VALUE="0.002" MAXLENGTH="10">
+<BR>
+<INPUT type="checkbox" NAME="PHI_BLAST">
+<a href="docs/pattern.html">Pattern for use in PHI-BLAST search</a>
+<INPUT TYPE="text" NAME ="PHI_PATTERN"  SIZE="35">
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<a href="docs/matrix_info.html">Matrix</a>
+<select name = "MAT_PARAM">
+    <option value = "PAM30	 9	 1"> PAM30 </option>
+    <option value = "PAM70	 10	 1"> PAM70 </option> 
+    <option value = "BLOSUM80	 10	 1"> BLOSUM80 </option>
+    <option selected value = "BLOSUM62	 11	 1"> BLOSUM62 </option>
+    <option value = "BLOSUM45	 14	 2"> BLOSUM45 </option>
+</select>
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">
+<HR>
+<!--
+<INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp;
+-->
+<INPUT TYPE="checkbox" NAME="OVERVIEW"  CHECKED> 
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> query-anchored with identities
+    <option value=2> query-anchored without identities
+    <option value=3> flat query-anchored with identities
+    <option value=4> flat query-anchored without identities
+    <option value=7> BLAST XML
+    <option value=9> Hit Table
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option> 100 
+    <option> 250 
+    <option selected> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option> 100 
+    <option> 250 
+    <option selected> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/psiblast.log b/network/wwwblast/psiblast.log
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/network/wwwblast/psiblast.log
diff --git a/network/wwwblast/psiblast.rc b/network/wwwblast/psiblast.rc
new file mode 100644
index 00000000..c136f0ff
--- /dev/null
+++ b/network/wwwblast/psiblast.rc
@@ -0,0 +1,28 @@
+# $Id: psiblast.rc,v 1.1 2002/08/06 19:03:52 dondosha Exp $
+#
+#================================================================
+#
+#     This is dynamic configuration file for WWW BLAST service
+#              All lines started from '#' are ignored.
+#           "//" string considered as start of comments
+#
+#     Author Sergei B. Shavirin
+#
+# $Revision: 1.1 $
+#
+#
+##################################################################
+#
+#
+# Number of CPUs to use for a single request
+#
+NumCpuToUse     4
+#
+# Here are list of combinations program/database, 
+# that allowed by BLAST service. Format: <program> <db> <db> ...
+#
+blastn test_na_db
+blastp test_aa_db
+blastx test_aa_db
+tblastn test_na_db
+tblastx test_na_db
diff --git a/network/wwwblast/psiblast_cs.cgi b/network/wwwblast/psiblast_cs.cgi
new file mode 100755
index 00000000..52104103
--- /dev/null
+++ b/network/wwwblast/psiblast_cs.cgi
@@ -0,0 +1,14 @@
+#!/bin/csh -f
+
+#
+# $Id: psiblast_cs.cgi,v 1.1 2002/08/06 19:03:52 dondosha Exp $
+#
+
+echo "Content-type: text/html"
+echo ""
+
+#setenv WWW_ROOT_PATH /blast
+#setenv DEBUG_COMMAND_LINE TRUE
+setenv BLASTDB db
+
+./psiblast_cs.REAL
diff --git a/network/wwwblast/psiblast_cs.html b/network/wwwblast/psiblast_cs.html
new file mode 100644
index 00000000..8ed8b88e
--- /dev/null
+++ b/network/wwwblast/psiblast_cs.html
@@ -0,0 +1,198 @@
+<!--
+/* $Id: psiblast_cs.html,v 1.3 2003/06/24 21:53:54 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: psiblast_cs.html,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.3 $
+*
+* File Description:
+*         Template for standalone PSI BLAST Web page
+*
+* $Log: psiblast_cs.html,v $
+* Revision 1.3  2003/06/24 21:53:54  dondosha
+* Changed WWW_BLAST_TYPE to BLAST_TYPE
+*
+* Revision 1.2  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.1  2002/08/06 19:03:52  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/psi_blast.gif" ISMAP> 
+
+<FORM ACTION="psiblast_cs.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<INPUT type="hidden" name = "BLAST_TYPE" value = "psiblast">
+<B>Choose <a href="docs/blast_databases.html">database</a> to use with PSI/PHI Blast:</B>&nbsp;&nbsp;
+<select name = "DATALIB">
+    <option VALUE = "test_aa_db"> test_aa_db
+    <option VALUE = "test_na_db"> test_na_db 
+</select>
+<input type="hidden" name = "PROGRAM" value="blastp">
+
+<!--
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+-->
+
+<P>
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+<INPUT TYPE="submit" VALUE="Search">&nbsp;&nbsp;
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQUENCE.focus();">
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+
+<P>Please read about <a href="/BLAST/fasta.html">FASTA</a> format description
+<HR>
+
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER"> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+<P>
+
+<INPUT TYPE="checkbox" NAME="TWEAK_PARAMETERS" CHECKED> <a href ="docs/composition.html">Composition-based statistics</a> &nbsp; &nbsp; &nbsp; &nbsp;
+<INPUT TYPE="checkbox" NAME="SMITH_WATERMAN"> Compute Smith-Waterman alignments
+<P>
+<a href="docs/newoptions.html#alignments">Expect value for inclusion in PSI-BLAST iteration 1</a>
+<INPUT TYPE="text" NAME ="E_THRESH" VALUE="0.002" MAXLENGTH="10">
+<BR>
+<INPUT type="checkbox" NAME="PHI_BLAST">
+<a href="docs/pattern.html">Pattern for use in PHI-BLAST search</a>
+<INPUT TYPE="text" NAME ="PHI_PATTERN"  SIZE="35">
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<a href="docs/matrix_info.html">Matrix</a>
+<select name = "MAT_PARAM">
+    <option value = "PAM30	 9	 1"> PAM30 </option>
+    <option value = "PAM70	 10	 1"> PAM70 </option> 
+    <option value = "BLOSUM80	 10	 1"> BLOSUM80 </option>
+    <option selected value = "BLOSUM62	 11	 1"> BLOSUM62 </option>
+    <option value = "BLOSUM45	 14	 2"> BLOSUM45 </option>
+</select>
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">
+<HR>
+
+<INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp;
+
+<INPUT TYPE="checkbox" NAME="OVERVIEW"  CHECKED> 
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> query-anchored with identities
+    <option value=2> query-anchored without identities
+    <option value=3> flat query-anchored with identities
+    <option value=4> flat query-anchored without identities
+    <option value=7> BLAST XML
+    <option value=9> Hit Table
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option> 100 
+    <option> 250 
+    <option selected> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option> 100 
+    <option> 250 
+    <option selected> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/readme.html b/network/wwwblast/readme.html
new file mode 100644
index 00000000..114e70a2
--- /dev/null
+++ b/network/wwwblast/readme.html
@@ -0,0 +1,460 @@
+<!-- $Id: readme.html,v 1.9 2003/06/24 21:53:54 dondosha Exp $ -->
+<HTML>
+<HEAD>
+<TITLE>Introduction to the Standalone WWW Blast server</TITLE>
+</HEAD>
+<BODY LINK="#0000ff" VLINK="#800080" BGCOLOR="#ffffff" ALINK="#660099">
+
+<P><!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN"></P>
+<P><HR></P>
+<H2 ALIGN="CENTER">Introduction to the Standalone WWW Blast server</H2>
+<P><HR></P>
+<H3>Index</H3>
+
+<UL>
+<LI><A HREF="#Inroduction">Introduction</A> </LI>
+<LI><A HREF="#Whatsnew">What's new in this revision?</A> </LI>
+<LI><A HREF="#Installation">Installation of the Standalone WWW server</A> </LI>
+<LI><A HREF="#Description_of_files">Description of files in the distribution</A> </LI>
+<LI><A HREF="#Configuration_of_databases">Configuration of BLAST databases</A> </LI>
+<LI><A HREF="#PSI_PHI_Notes">PSI/PHI Blast notes</A> </LI>
+<LI><A HREF="#CS_Notes">Client/server versions for Entrez lookup and taxonomy reports</A> </LI>
+<LI><a href="#Bl2Seq">Blast 2 sequences</a>
+<LI><A HREF="#XML_Output">XML output</A>
+<LI><A HREF="#OOF_blastx">Out of Frame BLASTX</A>
+<LI><A HREF="#RPS_blast">RPS Blast</A>
+<LI><A HREF="#Description_of_tags">Description of tags for main BLAST input page</A> </LI>
+<LI><A HREF="#Configuration_file">Server configuration file and logfile</A> </LI>
+<LI><A HREF="#Debugging">How to debug WWW Blast programs</A> </LI>
+</UL>
+
+<H3><A NAME="Inroduction">Introduction</A> </H3>
+<P>This standalone WWW BLAST server suite of programs was designed similar to the regular NCBI BLAST server and such command-line NCBI BLAST programs like "blastall", "blastpgp", "rpsblast" and "megablast". It incorporates most features, which exist in NCBI BLAST programs and should be relatively easy to use. This server does not support any request queuing and load balancing. As soon as the user hits a "Search" button, BLAST starts immediately if entered information is valid. So, this server is not intended to handle large load, which may exist in public service. Such queueing and loadbalancing however may be implemented using such products as Load Sharing Facility - "LSF" from <a href="http://www.platform.com">Platform Computing Corporation</a>. Interface to "LSF" was implemented in NCBI, however this was not included in this suite. Standalone server assumes that users have their own BLAST or RPS-BLAST database(s), that should be searched and want to have a simple WWW interface to such search. It is STRONLY recommended that user has experience in installation and running standalone NCBI BLAST programs. </P>
+<P>After files are uncompressed, server is ready to be used immediately. Any customizations to the program are welcomed and may be done by experienced programmers using source code, which is also provided. <P>Recompilation of the server executables requires that programmer has compiled NCBI toolkit libraries. This toolkit can be downloaded from the NCBI FTP web site: <A HREF="ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README.htm">ftp://ftp.ncbi.nih.gov</A> <BR>After the NCBI toolkit is compiled, user needs to edit the Makefile in the blast/Src directory, and define the NCBI variable in the top line of the Makefile, so it points to the root directory where the NCBI toolkit is located.</P>
+<H3><A NAME="Whatsnew">What's new in this revision?</A></H3>
+
+<TABLE BORDER=1>
+<TR VALIGN=top>
+<TD> May 9, 2003
+<TD>
+<UL>
+<LI> Cleaned the Makefile for recompiling the sources.
+<LI> Added discontiguous Mega BLAST options.
+<LI> Added option to choose a subsequence location for query.
+<LI> Added option to choose database genetic code.
+<LI> All binaries recompiled.
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> April 21, 2003
+<TD>
+<UL>
+<LI> Added instructions for recompilation of binaries from the source code to this readme file.
+<LI> Fixed a bug in processing of the configuration file that limited allowed number of databases.
+<LI> Added images for the Linkout and UniGene links from the BLAST output.
+<LI> Corrected paths to the graphical overview for PSI/PHI BLAST output.
+<LI> All binaries recompiled with the newest version of the NCBI C toolkit libraries.
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> February 10, 2003
+<TD>
+<UL>
+<LI> Added support for multi-query XML output.
+<LI> All binaries recompiled.
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> December 2, 2002
+<TD>
+<UL>
+<LI> All binaries recompiled with the newest version of the toolkit. 
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> August 6, 2002
+<TD>
+<UL>
+<LI> Recompiled all binaries to include recent bug fixes.
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> June 18, 2002
+<TD>
+<UL>
+<LI> Removed limit on the total length of database names. 
+<LI> Removed xmlblast.cgi and other unneeded XML related files. 
+<LI> Recompiled all programs.
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> January 11, 2002
+<TD>
+<UL>
+<LI> Removed formatdb, makemat and copymat binaries from the archive - those should be taken from the <a href="ftp://ncbi.nlm.nih.gov/blast/executables">NCBI BLAST executables archive</a>
+<LI> Added tabular output format
+<LI> Added option to mask lower case in query
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> May, 2 2001 
+<TD>
+<UL>
+<LI> No major changes. All programs have been recompiled and made synchronous to the latest NCBI tookit release.
+</UL>
+</TR>
+<TR VALIGN=top>
+<TD> November 3, 2000 
+<TD>
+<UL>
+<LI> <a href="#Bl2Seq">Blast 2 sequences</a> was added
+</UL>
+</TR><TR VALIGN=top>
+<TD> October, 19 2000 
+<TD>
+<UL>
+<LI> <a href="#RPS_blast">RPS Blast</a> was added
+<LI> <a href=#OOF_blastx>Out of Frame BLASTX</a> (OOF) now available for testing and suggestions.
+</UL>
+</TR><TR VALIGN=top>
+<TD> September, 28 2000 
+<TD>
+<UL>
+<LI> Added possibility to limit search to results of Entrez query (Regular
+     client/server BLAST)
+</UL>
+</TR><TR VALIGN=top>
+<TD> September, 11 2000 
+<TD>
+<UL>
+<LI> Added <A HREF="docs/megablast_readme.html">MEGABLAST</A> search.
+<LI> Added possibility to have multiple FASTA query input - batch searches 
+     with multiple graphical overviews. (Regular BLAST)
+</UL>
+</TR><TR VALIGN=top>
+<TD> August, 22 2000 
+<TD>
+<UL>
+<LI> Added new advanced statistics to PSI Blast and ability to produce Smith-Waterman alignments
+<LI>Added support for XML output.
+</UL>
+</TR><TR VALIGN=top>
+<TD> May, 17 2000 
+<TD>
+<UL>
+<LI>PSI and PHI Blast were added to this distribution
+<LI>Added support for client/server interface for gi/accesion
+     lookups using Entrez
+<LI>Added possibility to print Taxonomy reports
+<LI>Added option to print alternative alignment with specific color schema
+</UL>
+</TR><TR VALIGN=top>
+<TD> March, 20 2000 
+<TD>
+<UL>
+<LI> Initial revision
+</UL>
+</TR>
+</TABLE>
+
+<H3><A NAME="Installation">Installation of the Standalone WWW server</A></H3>
+<P>After downloading the file wwwblast.Your_platform.tar.gz to your computer, place it into document directory of HTTPD server and uncompress it by </P>
+<PRE>
+    gzip -d wwwblast.Your_platform.tar.gz
+    tar -xvpf wwwblast.Your_platform.tar</PRE>
+<P>Please note that parameter "p" in tar options is significant - it will preserve file access options stored in the distribution. Temporary directory for BLAST overview images (TmpGifs) should have 777 permission, and logfiles (wwwblast.log and psiblast.log) should have 666. </P>
+<P>After you have uncompressed the distribution file, "blast" directory will be created. You can access sample BLAST HTML input forms using URLs:
+<UL> 
+<LI>http://your_hostname/blast/blast.html
+<LI>http://your_hostname/blast/blast_cs.html
+<LI>http://your_hostname/blast/psiblast.html
+<LI>http://your_hostname/blast/psiblast_cs.html
+<LI>http://your_hostname/blast/megablast.html
+<LI>http://your_hostname/blast/megablast_cs.html
+<LI>http://your_hostname/blast/wblast2.html
+<LI>http://your_hostname/blast/wblast2_cs.html
+</UL>
+This distribution comes with 2 BLAST databases: "test_aa_db" - sample protein database and "test_na_db" - sample nucleotide database. These databases are configured to be searchable immediately with compatible BLAST programs. </P>
+<H3><A NAME="Description_of_files">Description of files in the distribution</A></H3>
+
+<UL>
+<LI>Root directory (<B>./blast</B>): </LI></UL>
+
+Files with suffix "*_cs.*" are analogous to the files without such suffix,
+with added capability to make client/server Entrez lookups for sequence
+gis and accessions.
+<P>
+<TABLE CELLSPACING=0 BORDER=0>
+<TR><TD VALIGN="MIDDLE">
+<P><I>blast.cgi, blast_cs.cgi</I></TD>
+<TD>
+<P>- BLAST search start-up C-shell files</TD>
+</TR>
+<TR><TD>
+<P><I>.nlmstmanrc</I></TD>
+<TD>
+<P>- Configuration file for the graphical overview image (do not edit!)</TD>
+</TR>
+<TR><TD>
+<I><P>blast.html, blast_cs.html</I></TD>
+<TD>
+<P>- sample BLAST search input HTML forms</TD>
+</TR>
+<TR><TD>
+<I><P>megablast.html, megablast_cs.html</I></TD>
+<TD>
+<P>- sample MEGABLAST search input HTML forms</TD>
+</TR>
+<TR><TD>
+<I><P>rpsblast.html, rpsblast_cs.html</I></TD>
+<TD>
+<P>- sample RPS BLAST search input HTML forms</TD>
+</TR>
+<TR><TD>
+<I><P>blast.rc</I></TD>
+<TD>
+<P>- <A HREF="#Configuration_file">Default configuration file</A> for the WWW BLAST server</TD>
+</TR>
+<TR><TD>
+<I><P>psiblast.rc</I></TD>
+<TD>
+<P>- <A HREF="#Configuration_file">Default configuration file</A> for the PSI/PHI WWW BLAST server</TD>
+</TR>
+<TR><TD>
+<P><I>psiblast.cgi, psiblast_cs.cgi</I></TD>
+<TD>
+<P>- PSI/PHI BLAST search start-up C-shell files</TD>
+</TR>
+<TR><TD>
+<I><P>psiblast.html, psiblast_cs.html</I></TD>
+<TD>
+<P>- sample PSI/PHI BLAST search input HTML forms</TD>
+</TR>
+<TR><TD>
+<I><P>psiblast.REAL, psiblast_cs.REAL</I></TD>
+<TD>
+<P>- Main PSI/PHI BLAST server executables</TD>
+</TR>
+<TR><TD>
+<I><P>wblast2.html, wblast2_cs.html</I></TD>
+<TD>
+<P>- sample BLAST 2 sequences search input HTML forms</TD>
+</TR>
+<TR><TD>
+<I><P>wblast2.REAL, wblast2_cs.REAL</I></TD>
+<TD>
+<P>- Main BLAST 2 sequences server executables</TD>
+</TR>
+<TR><TD>
+<I><P>bl2bag.cgi</I></TD>
+<TD>
+<P>- CGI used to create 2 sequences alignment image on the fly</TD>
+</TR>
+<TR><TD>
+<I><P>blast_form.map</I></TD>
+<TD>
+<P>- Auxiliary map file for the front BLAST image</TD>
+</TR>
+<TR><TD>
+<I><P>nph-viewgif.cgi</I></TD>
+<TD>
+<P>- CGI program used to view and delete overview images</TD>
+</TR>
+<TR><TD>
+<I><P>readme.html</I></TD>
+<TD>
+<P>- this documentation</TD>
+</TR>
+<TR><TD>
+<I><P>wwwblast.log</I></TD>
+<TD>
+<P>- default logfile</TD>
+</TR>
+<TR><TD>
+<I><P>psiblast.log</I></TD>
+<TD>
+<P>- default PSI/PHI Blast logfile</TD>
+</TR>
+<TR><TD>
+<I><P>ncbi_blast.rc</I></TD>
+<TD>
+<P>- sample file for full NCBI set of databases</TD>
+</TR>
+</TABLE>
+
+<UL>
+<B><LI>./data</B> directory - matrices used in BLAST search </LI>
+<B><LI>./db</B> directory. - Files of test BLAST and RPS-BLAST databases. </LI>
+<B><LI>./docs:</B> - HTML pages used in sample BLAST search input pages </LI>
+<B><LI>./images</B> - images used in the sample BLAST search input pages </LI>
+<B><LI>./Src</B> - source directory for the WWW BLAST server. </LI>
+<B><LI>./Src/XML</B> - source directory for creation of files related to the XML output.
+<UL>
+    <LI> blstxml.asn - ASN.1 definition for Blast XML
+    <LI> blstxml.dtd - corresponding DTD
+</UL>
+
+<B><LI>./TmpGifs</B> - storage for temporary BLAST overview gif files </LI></UL>
+
+<H3><A NAME="Configuration_of_databases">Configuration of BLAST databases</A></H3>
+<P>To set up databases for the standalone WWW BLAST server, it is necessary to follow these steps: </P>
+<OL>
+
+<LI>Put a file with concatenated FASTA entries in the "./db" directory </LI>
+<LI>Run "formatdb" program, available from the <a href="ftp://ncbi.nlm.nih.gov/blast/executables">NCBI ftp site</a> to format the database. </LI>
+<LI>Add name of the database into <A HREF="#Configuration_file">server configuration file</A> </LI>
+<LI>Add name of the database into (PSI/PHI) WWW BLAST search form </LI></OL>
+
+<H3><A NAME="PSI_PHI_Notes">PSI/PHI Blast notes</A> </H3>
+There is one significant feature of the PSI/PHI Blast server: FASTA
+files from which the BLAST databases are formatted should have GI numbers in all 
+sequence ids. This is almost always true for FASTA files from the NCBI FTP site.
+Local databases may not be used with this version of PSI/PHI Blast unless
+they have "&gt;gi|12345..." prefix in the definition line.
+<P>
+Databases for the PSI/PHI Blast should always be created with formatdb using
+the "-o T" flag. Test database "test_aa_db" was created using this flag and
+database "test_na_db" was created without this flag.
+<P>
+If this distribution is installed not in the "/blast" directory under HTTPD
+documents root directory, than path to the distribution should be set
+by an environment variable WWW_ROOT_PATH in the file psiblast.cgi or psiblast_cs.cgi
+<H3><A NAME="CS_Notes">Client/server version for Entrez lookup and taxonomy reports</A> </H3>
+Regular Blast, PSI/PHI Blast, MegaBlast and Blast 2 Sequences have client/server versions for
+Entrez gi/accession lookups and printing Taxonomy reports. Configuration of
+client/server interface from the user to NCBI should be done the same way as for any
+other client/server program to NCBI. If program "blastcl3" works without
+problems, this server should work OK as well. If user has firewall - default
+configuration will definitely fail to work properly and this case will
+require special configuration. If user has problems with such configuration,
+one should write to
+<a href="mailto:info@ncbi.nlm.nih.gov">info@ncbi.nlm.nih.gov</a>
+ for further assistance.
+<H3><A NAME="XML_Output">XML output</A></H3>
+Possibility to produce XML output was added to this server. XML definition
+of BLAST output is tied to the simple ASN.1 specification designed for this
+case. These definitions  may be found in the directory ./Src/XML. Any 
+recommendations on improvements to this (possible) standard may be sent to 
+<a href = "mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> 
+XML may be printed by setting "Alignment view" in blast.html or (blast_cs.html)
+page to "BLAST XML".
+Resulting page will look empty - but if you open the page source (in Netscape -
+View -> Page source) - you will see the complete XML document.
+<H3><A NAME="Bl2Seq">Blast 2 sequences</A></H3>
+Blast 2 sequences program was initially written by Tatiana Tatusova and
+Tom Madden and was presented in the article: Tatiana A. Tatusova, 
+Thomas L. Madden (1999), "Blast 2 sequences - a new tool for
+comparing protein and nucleotide sequences", 
+<A HREF = "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10339815&form=6&db=m&Dopt=b">FEMS Microbiol Lett. 174:247-250</A>.
+The standalone WWW version of the program mirrors the <a href="http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html">NCBI Blast 2 Sequences</a> web page. 
+<H3><A NAME="RPS_blast">RPS Blast</A></H3>
+RPS Blast or "Reversed Position Specific BLAST" is a
+very fast alternative to the program <a href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10745990&dopt=Abstract">IMPALA</a>. It has the same general
+objective - to compare a sequence to a collection of conserved domains (aka motifs, profiles, HMMs).
+RPS Blast has a completely different implementation that has
+increased the speed of profiles search 10 to 100 times depending on search
+conditions in comarison to IMPALA. RPS Blast has an option to perform a translated search of DNA sequences against these conserved domains. 
+Currently RPS Blast is one of the tools chosen to annotate human 
+genome at NCBI and is the basis for the <a href ="http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi">CDD Blast search</a> page.
+<P>
+Databases for RPS blast are hardware dependent - for speed reasons. Hence 
+they are different for big/little endian platforms.
+<P>
+To build RPS database it is necessary to follow the procedure explained in
+the file "README.rps", that comes with this distribution.
+There is a small RPS database available for testing. This database is a part
+of a real NCBI database used in CDD search page. Full NCBI database is
+available in platform-independent form from FTP site.
+
+<H3><A NAME="OOF_blastx">Out of Frame BLASTX</A></H3>
+The OOF version of the blastx program finds alignments between a nucleotide 
+sequence translated into 3 frames and protein sequences, in which query sequence 
+frames can be shifted within one alignment. The algorithm and low-level alignment 
+functions were written by Zheng Zhang, currently at <a href="http://www.paracel.com">Paracel Inc.</a>, and incorporated into regular BLAST API by Sergei Shavirin. 
+<P>
+XML and tabular output are not yet implemented for the OOF alignments.
+<H3><A NAME="Description_of_tags">Description of tags for the main BLAST input page</A></H3>
+<P>This standalone server has a tag convention analogous to the regular NCBI BLAST server. Sample BLAST search forms may be changed to accommodate particular needs of the user in the custom search. Here is the list of these tags and their meaning. If some tag is missing from the search input page, it will take a default value. Exceptions are tags PROGRAM, DATALIB and SEQUENCE (or SEQFILE), that should always be set. </P>
+
+<UL>
+<B><LI>PROGRAM</B> - name of the BLAST program. Supported values include programs: blastn, blastp, blastx, tblastx and tblastn </LI>
+<B><LI>DATALIB</B> - name of the database(s) to search. This implementation includes possibility to use multiple databases. To use multiple databases several "DATALIB" tags should be used on the page for example using checkboxes (look for example at <A HREF="http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome.html">Microbial Genomes Blast Databases BLAST</A> at NCBI). Note, that all of these databases should be properly written in the server configuration file. </LI>
+<B><LI>SEQUENCE</B> and <B>SEQFILE</B> - these tags used to pass sequence. First SEQUENCE tag is used for the input sequence. If it is missing, the SEQFILE tag is used instead. </LI>
+<B><LI>UNGAPPED_ALIGNMENT</B> - default BLAST search is a gapped search; this tag, if set, will turn gapped alignment off. </LI>
+<B><LI>MAT_PARAM</B> used to set 3 parameters at the same time. Value for this tag should be in format "<mat_name> <d1><d2>" where mat_name - string name of the matrix (BLOSUM62, etc), d1 - integer for cost to open gap and d2 - cost to extend gap (-G and -E parameters in blastall respectably) </LI>
+<B><LI>GAP_OPEN</B> - set value for cost to open gap - 0 or missing tag invoked default behavior </LI>
+<B><LI>GAP_EXTEND</B> - set value for cost to extend gap - 0 or missing tag invoked default behavior </LI>
+<B><LI>X_DROPOFF</B> - Dropoff (X) for blast extensions in bits (default if zero) (-y parameter in "blastpgp" program) </LI>
+<B><LI>GENETIC_CODE</B> - Query Genetic code to use (for blastx only) </LI>
+<B><LI>THRESHOLD_2</B> - Threshold for extending hits in second pass in multipass model search </LI>
+<B><LI>MATRIX</B> - Matrix (default is BLOSUM62) (-M in blastall) </LI>
+<B><LI>EXPECT</B> - Expectation value (-e in blastall) </LI>
+<B><LI>NUM_OF_BITS</B> - Number of bits to trigger gapping (-N in blastpgp) </LI>
+<B><LI>NCBI_GI</B> - If formated database use SeqIds in the NCBI format this option will turn printing of gis together with accessions. </LI>
+<B><LI>FILTER</B> - Multiple instances of values of this tag are concatenated and passed to the engine as "filter_string" ("L" for low complexity and "m" if filter should be set for lookup table only) - any letter will turn default filtering on - DUST for nucleotides and SEG for proteins (-F in blastall) </LI>
+<B><LI>DESCRIPTIONS</B> - Number of one-line descriptions in the output (-v in blastall) </LI>
+<B><LI>ALIGNMENTS</B> - Number of alignments to show (-b in blastall) </LI>
+<B><LI>COLOR_SCHEMA</B> - Color schema to use in printing of alternative alignment. This option is valid only for blastp and blastn programs. If set - it will
+override option set by "ALIGNMENT_VIEW" </LI>
+<B><LI>TAX_BLAST</B> - Print taxonomy reports. This option is valid only for
+client/server version of regular Blast </LI>
+<B><LI>XML_OUTPUT</B> - Print XML Blast output. All other alignment view options will be disabled </LI>
+<B><LI>ENTREZ_QUERY</B> - Limit search to results of Entrez query. Only for 
+client/server version </LI>
+<B><LI>RPSBLAST</B> - This tag with turn "blastp" or "blastx" search into RPS Blast search for the rps blast database. </LI>
+<B><LI>OOF_ALIGN</B> -This flag if set to non-zero digit will turn on OOF alignment for "blastx" and will set frame shift penalty to this value. </LI>
+<B><LI>OTHER_ADVANCED</B> - this tag allows to input string analogous to the command line parameters of blastall. Setting parameter in OTHER_ADVANCED tag will override all other settings of this parameter. Supported options include: </LI>
+<UL>
+<B><LI>-G</B> gap open cost </LI>
+<B><LI>-E</B> gap extend cost </LI>
+<B><LI>-q</B> penalty for nucleotide mismatch </LI>
+<B><LI>-r</B> reward for nucleotide match </LI>
+<B><LI>-e</B> expect value </LI>
+<B><LI>-W</B> wordsize </LI>
+<B><LI>-v</B> Number of descriptions to print </LI>
+<B><LI>-b</B> Number of alignments to show </LI>
+<B><LI>-K</B> Number of best hits from a region to keep </LI>
+<B><LI>-Y</B> effective search space </LI></UL>
+
+<B><LI>ALIGNMENT_VIEW</B> - will set type of alignment to show. Available options include: </LI>
+
+<UL>
+<LI>0 - Pairwise </LI>
+<LI>1 - query-anchored with identities </LI>
+<LI>2 - query-anchored without identities </LI>
+<LI>3 - flat query-anchored with identities </LI>
+<LI>4 - flat query-anchored without identities </LI>
+<LI>7 - BLAST XML (equivalent to setting the XML_OUTPUT tag)</LI>
+<LI>9 - Hit Table - to produce tabular output
+</UL>
+
+<B><LI>OVERVIEW</B> - used to turn on or off printing of alignment overview image </LI>
+<B><LI>BLAST_TYPE</B> - a special tag to distinguish different BLAST search types. See the description of a configuration file. </LI></UL>
+
+<H3><A NAME="Configuration_file">Server configuration file and logfile</A></H3>
+<P>Default configuration file is "blast.rc" and logfile "wwwblast.log". Setting tag BLAST_TYPE to specific value may change these names. This is useful if few different search input pages use the same CGI search engine, but significantly different by content and priorities. A sample configuration file comes with this distribution: </P>
+This file will set how many CPUs will be used in the BLAST search and what databases may be used with what programs. Logfile currently stores only limited information but also may be updated by programmers to store more values in it. Please note, that usually HTTPD servers run by accounts that do not have write access to disk, so the logfile permission should be set to 666. </P>
+<H3><A NAME="Debugging">How to debug WWW Blast programs</A></H3>
+
+There is a way to debug these programs.
+
+<OL>
+<LI> Add line "setenv DEBUG_COMMAND_LINE TRUE" into the *.cgi file
+   (uncomment it)
+<LI> Run search that results in the problem - this should create a
+   file "/tmp/__web.in" in the "/tmp" directory.
+<LI> Set all necessary environment variables on the command line (BLASTDB at least)
+   and run from command-line: "blast.REAL &lt; /tmp/__web.in"
+</OL>
+This should do your problematic search without WWW. If this resulted
+in coredump - you may look into the core file with:
+<P>
+dbx blast.REAL core
+<P>
+and then use command "where" to print stack.
+
+<P><HR></P>
+<ADDRESS><A HREF="mailto:blast-help@ncbi.nlm.nih.gov">BLAST Help Desk</A></ADDRESS>
+<P><!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->Last modified: Fri Jan 11, 2002 <!-- hhmts end --></P></BODY>
+</HTML>
diff --git a/network/wwwblast/readme.txt b/network/wwwblast/readme.txt
new file mode 100644
index 00000000..a4d89b55
--- /dev/null
+++ b/network/wwwblast/readme.txt
@@ -0,0 +1,527 @@
+------------------------------------------------------------------------
+
+
+    Introduction to the Standalone WWW Blast server
+
+------------------------------------------------------------------------
+
+
+      Index
+
+    * Introduction <#Inroduction>
+    * What's new in this revision? <#Whatsnew>
+    * Installation of the Standalone WWW server <#Installation>
+    * Description of files in the distribution <#Description_of_files>
+    * Configuration of BLAST databases <#Configuration_of_databases>
+    * PSI/PHI Blast notes <#PSI_PHI_Notes>
+    * Client/server versions for Entrez lookup and taxonomy reports
+      <#CS_Notes>
+    * Blast 2 sequences <#Bl2Seq>
+    * XML output <#XML_Output>
+    * Out of Frame BLASTX <#OOF_blastx>
+    * RPS Blast <#RPS_blast>
+    * Description of tags for main BLAST input page <#Description_of_tags>
+    * Server configuration file and logfile <#Configuration_file>
+    * How to debug WWW Blast programs <#Debugging>
+
+
+      Introduction
+
+This standalone WWW BLAST server suite of programs was designed similar
+to the regular NCBI BLAST server and such command-line NCBI BLAST
+programs like "blastall", "blastpgp", "rpsblast" and "megablast". It
+incorporates most features, which exist in NCBI BLAST programs and
+should be relatively easy to use. This server does not support any
+request queuing and load balancing. As soon as the user hits a "Search"
+button, BLAST starts immediately if entered information is valid. So,
+this server is not intended to handle large load, which may exist in
+public service. Such queueing and loadbalancing however may be
+implemented using such products as Load Sharing Facility - "LSF" from
+Platform Computing Corporation <http://www.platform.com>. Interface to
+"LSF" was implemented in NCBI, however this was not included in this
+suite. Standalone server assumes that users have their own BLAST or
+RPS-BLAST database(s), that should be searched and want to have a simple
+WWW interface to such search. It is STRONLY recommended that user has
+experience in installation and running standalone NCBI BLAST programs.
+
+After files are uncompressed, server is ready to be used immediately.
+Any customizations to the program are welcomed and may be done by
+experienced programmers using source code, which is also provided.
+
+Recompilation of the server executables requires that programmer has
+compiled NCBI toolkit libraries. This toolkit can be downloaded from the
+NCBI FTP web site: ftp://ftp.ncbi.nih.gov
+<ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/README.htm>
+After the NCBI toolkit is compiled, user needs to edit the Makefile in
+the blast/Src directory, and define the NCBI variable in the top line of
+the Makefile, so it points to the root directory where the NCBI toolkit
+is located.
+
+
+      What's new in this revision?
+
+May 9, 2003
+
+    * Cleaned the Makefile for recompiling the sources.
+    * Added discontiguous Mega BLAST options.
+    * Added option to choose a subsequence location for query.
+    * Added option to choose database genetic code.
+* All binaries recompiled.
+
+April 21, 2003
+
+    * Added instructions for recompilation of binaries from the source
+      code to this readme file.
+    * Fixed a bug in processing of the configuration file that limited
+      allowed number of databases.
+    * Added images for the Linkout and UniGene links from the BLAST output.
+    * Corrected paths to the graphical overview for PSI/PHI BLAST output.
+    * All binaries recompiled with the newest version of the NCBI C
+toolkit libraries.
+
+February 10, 2003
+
+    * Added support for multi-query XML output.
+* All binaries recompiled.
+
+December 2, 2002
+
+* All binaries recompiled with the newest version of the toolkit.
+
+August 6, 2002
+
+* Recompiled all binaries to include recent bug fixes.
+
+June 18, 2002
+
+    * Removed limit on the total length of database names.
+    * Removed xmlblast.cgi and other unneeded XML related files.
+* Recompiled all programs.
+
+January 11, 2002
+
+    * Removed formatdb, makemat and copymat binaries from the archive -
+      those should be taken from the NCBI BLAST executables archive
+      <ftp://ncbi.nlm.nih.gov/blast/executables>
+    * Added tabular output format
+* Added option to mask lower case in query
+
+May, 2 2001
+
+    * No major changes. All programs have been recompiled and made
+synchronous to the latest NCBI tookit release.
+
+November 3, 2000
+
+* Blast 2 sequences <#Bl2Seq> was added
+
+October, 19 2000
+
+    * RPS Blast <#RPS_blast> was added
+    * Out of Frame BLASTX <#OOF_blastx> (OOF) now available for testing
+and suggestions.
+
+September, 28 2000
+
+    * Added possibility to limit search to results of Entrez query
+(Regular client/server BLAST)
+
+September, 11 2000
+
+    * Added MEGABLAST <docs/megablast_readme.html> search.
+    * Added possibility to have multiple FASTA query input - batch
+searches with multiple graphical overviews. (Regular BLAST)
+
+August, 22 2000
+
+    * Added new advanced statistics to PSI Blast and ability to produce
+      Smith-Waterman alignments
+* Added support for XML output.
+
+May, 17 2000
+
+    * PSI and PHI Blast were added to this distribution
+    * Added support for client/server interface for gi/accesion lookups
+      using Entrez
+    * Added possibility to print Taxonomy reports
+    * Added option to print alternative alignment with specific color
+schema
+
+March, 20 2000
+
+* Initial revision
+
+
+      Installation of the Standalone WWW server
+
+After downloading the file wwwblast.Your_platform.tar.gz to your
+computer, place it into document directory of HTTPD server and
+uncompress it by
+
+    gzip -d wwwblast.Your_platform.tar.gz
+    tar -xvpf wwwblast.Your_platform.tar
+
+Please note that parameter "p" in tar options is significant - it will
+preserve file access options stored in the distribution. Temporary
+directory for BLAST overview images (TmpGifs) should have 777
+permission, and logfiles (wwwblast.log and psiblast.log) should have 666.
+
+After you have uncompressed the distribution file, "blast" directory
+will be created. You can access sample BLAST HTML input forms using URLs:
+
+    * http://your_hostname/blast/blast.html
+    * http://your_hostname/blast/blast_cs.html
+    * http://your_hostname/blast/psiblast.html
+    * http://your_hostname/blast/psiblast_cs.html
+    * http://your_hostname/blast/megablast.html
+    * http://your_hostname/blast/megablast_cs.html
+    * http://your_hostname/blast/wblast2.html
+* http://your_hostname/blast/wblast2_cs.html
+
+This distribution comes with 2 BLAST databases: "test_aa_db" - sample
+protein database and "test_na_db" - sample nucleotide database. These
+databases are configured to be searchable immediately with compatible
+BLAST programs.
+
+
+      Description of files in the distribution
+
+* Root directory (./blast):
+
+Files with suffix "*_cs.*" are analogous to the files without such
+suffix, with added capability to make client/server Entrez lookups for
+sequence gis and accessions.
+
+blast.cgi, blast_cs.cgi
+
+- BLAST search start-up C-shell files
+
+.nlmstmanrc
+
+- Configuration file for the graphical overview image (do not edit!)
+
+blast.html, blast_cs.html
+
+- sample BLAST search input HTML forms
+
+megablast.html, megablast_cs.html
+
+- sample MEGABLAST search input HTML forms
+
+rpsblast.html, rpsblast_cs.html
+
+- sample RPS BLAST search input HTML forms
+
+blast.rc
+
+- Default configuration file <#Configuration_file> for the WWW BLAST server
+
+psiblast.rc
+
+- Default configuration file <#Configuration_file> for the PSI/PHI WWW
+BLAST server
+
+psiblast.cgi, psiblast_cs.cgi
+
+- PSI/PHI BLAST search start-up C-shell files
+
+psiblast.html, psiblast_cs.html
+
+- sample PSI/PHI BLAST search input HTML forms
+
+psiblast.REAL, psiblast_cs.REAL
+
+- Main PSI/PHI BLAST server executables
+
+wblast2.html, wblast2_cs.html
+
+- sample BLAST 2 sequences search input HTML forms
+
+wblast2.REAL, wblast2_cs.REAL
+
+- Main BLAST 2 sequences server executables
+
+bl2bag.cgi
+
+- CGI used to create 2 sequences alignment image on the fly
+
+blast_form.map
+
+- Auxiliary map file for the front BLAST image
+
+nph-viewgif.cgi
+
+- CGI program used to view and delete overview images
+
+readme.html
+
+- this documentation
+
+wwwblast.log
+
+- default logfile
+
+psiblast.log
+
+- default PSI/PHI Blast logfile
+
+ncbi_blast.rc
+
+- sample file for full NCBI set of databases
+
+    * ./data
+    * directory - matrices used in BLAST search ./db
+    * directory. - Files of test BLAST and RPS-BLAST databases. ./docs:
+    * - HTML pages used in sample BLAST search input pages ./images
+    * - images used in the sample BLAST search input pages ./Src
+    * - source directory for the WWW BLAST server. ./Src/XML
+      - source directory for creation of files related to the XML output.
+          o blstxml.asn - ASN.1 definition for Blast XML
+    o blstxml.dtd - corresponding DTD
+    * ./TmpGifs
+- storage for temporary BLAST overview gif files
+
+
+      Configuration of BLAST databases
+
+To set up databases for the standalone WWW BLAST server, it is necessary
+to follow these steps:
+
+   1. Put a file with concatenated FASTA entries in the "./db" directory
+   2. Run "formatdb" program, available from the NCBI ftp site
+      <ftp://ncbi.nlm.nih.gov/blast/executables> to format the database.
+   3. Add name of the database into server configuration file
+      <#Configuration_file>
+   4. Add name of the database into (PSI/PHI) WWW BLAST search form 
+
+
+      PSI/PHI Blast notes
+
+There is one significant feature of the PSI/PHI Blast server: FASTA
+files from which the BLAST databases are formatted should have GI
+numbers in all sequence ids. This is almost always true for FASTA files
+from the NCBI FTP site. Local databases may not be used with this
+version of PSI/PHI Blast unless they have ">gi|12345..." prefix in the
+definition line.
+
+Databases for the PSI/PHI Blast should always be created with formatdb
+using the "-o T" flag. Test database "test_aa_db" was created using this
+flag and database "test_na_db" was created without this flag.
+
+If this distribution is installed not in the "/blast" directory under
+HTTPD documents root directory, than path to the distribution should be
+set by an environment variable WWW_ROOT_PATH in the file psiblast.cgi or
+psiblast_cs.cgi
+
+
+      Client/server version for Entrez lookup and taxonomy reports
+
+Regular Blast, PSI/PHI Blast, MegaBlast and Blast 2 Sequences have
+client/server versions for Entrez gi/accession lookups and printing
+Taxonomy reports. Configuration of client/server interface from the user
+to NCBI should be done the same way as for any other client/server
+program to NCBI. If program "blastcl3" works without problems, this
+server should work OK as well. If user has firewall - default
+configuration will definitely fail to work properly and this case will
+require special configuration. If user has problems with such
+configuration, one should write to info@ncbi.nlm.nih.gov
+<mailto:info@ncbi.nlm.nih.gov> for further assistance.
+
+
+      XML output
+
+Possibility to produce XML output was added to this server. XML
+definition of BLAST output is tied to the simple ASN.1 specification
+designed for this case. These definitions may be found in the directory
+./Src/XML. Any recommendations on improvements to this (possible)
+standard may be sent to blast-help@ncbi.nlm.nih.gov
+<mailto:blast-help@ncbi.nlm.nih.gov> XML may be printed by setting
+"Alignment view" in blast.html or (blast_cs.html) page to "BLAST XML".
+Resulting page will look empty - but if you open the page source (in
+Netscape - View -> Page source) - you will see the complete XML document.
+
+
+      Blast 2 sequences
+
+Blast 2 sequences program was initially written by Tatiana Tatusova and
+Tom Madden and was presented in the article: Tatiana A. Tatusova, Thomas
+L. Madden (1999), "Blast 2 sequences - a new tool for comparing protein
+and nucleotide sequences", FEMS Microbiol Lett. 174:247-250
+<http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=10339815&form=6&db=m&Dopt=b>.
+The standalone WWW version of the program mirrors the NCBI Blast 2
+Sequences <http://www.ncbi.nlm.nih.gov/blast/bl2seq/bl2.html> web page.
+
+
+      RPS Blast
+
+RPS Blast or "Reversed Position Specific BLAST" is a very fast
+alternative to the program IMPALA
+<http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10745990&dopt=Abstract>.
+It has the same general objective - to compare a sequence to a
+collection of conserved domains (aka motifs, profiles, HMMs). RPS Blast
+has a completely different implementation that has increased the speed
+of profiles search 10 to 100 times depending on search conditions in
+comarison to IMPALA. RPS Blast has an option to perform a translated
+search of DNA sequences against these conserved domains. Currently RPS
+Blast is one of the tools chosen to annotate human genome at NCBI and is
+the basis for the CDD Blast search
+<http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi> page.
+
+Databases for RPS blast are hardware dependent - for speed reasons.
+Hence they are different for big/little endian platforms.
+
+To build RPS database it is necessary to follow the procedure explained
+in the file "README.rps", that comes with this distribution. There is a
+small RPS database available for testing. This database is a part of a
+real NCBI database used in CDD search page. Full NCBI database is
+available in platform-independent form from FTP site.
+
+
+      Out of Frame BLASTX
+
+The OOF version of the blastx program finds alignments between a
+nucleotide sequence translated into 3 frames and protein sequences, in
+which query sequence frames can be shifted within one alignment. The
+algorithm and low-level alignment functions were written by Zheng Zhang,
+currently at Paracel Inc. <http://www.paracel.com>, and incorporated
+into regular BLAST API by Sergei Shavirin.
+
+XML and tabular output are not yet implemented for the OOF alignments.
+
+
+      Description of tags for the main BLAST input page
+
+This standalone server has a tag convention analogous to the regular
+NCBI BLAST server. Sample BLAST search forms may be changed to
+accommodate particular needs of the user in the custom search. Here is
+the list of these tags and their meaning. If some tag is missing from
+the search input page, it will take a default value. Exceptions are tags
+PROGRAM, DATALIB and SEQUENCE (or SEQFILE), that should always be set.
+
+    * PROGRAM
+      - name of the BLAST program. Supported values include programs:
+    * blastn, blastp, blastx, tblastx and tblastn DATALIB
+      - name of the database(s) to search. This implementation includes
+      possibility to use multiple databases. To use multiple databases
+      several "DATALIB" tags should be used on the page for example
+      using checkboxes (look for example at Microbial Genomes Blast
+      Databases BLAST
+      <http://www.ncbi.nlm.nih.gov/Microb_blast/unfinishedgenome.html>
+      at NCBI). Note, that all of these databases should be properly
+    * written in the server configuration file. SEQUENCE
+      and SEQFILE - these tags used to pass sequence. First SEQUENCE tag
+      is used for the input sequence. If it is missing, the SEQFILE tag
+    * is used instead. UNGAPPED_ALIGNMENT
+      - default BLAST search is a gapped search; this tag, if set, will
+    * turn gapped alignment off. MAT_PARAM
+      used to set 3 parameters at the same time. Value for this tag
+      should be in format " " where mat_name - string name of the matrix
+      (BLOSUM62, etc), d1 - integer for cost to open gap and d2 - cost
+    * to extend gap (-G and -E parameters in blastall respectably) GAP_OPEN
+      - set value for cost to open gap - 0 or missing tag invoked
+    * default behavior GAP_EXTEND
+      - set value for cost to extend gap - 0 or missing tag invoked
+    * default behavior X_DROPOFF
+      - Dropoff (X) for blast extensions in bits (default if zero) (-y
+    * parameter in "blastpgp" program) GENETIC_CODE
+    * - Query Genetic code to use (for blastx only) THRESHOLD_2
+      - Threshold for extending hits in second pass in multipass model
+    * search MATRIX
+    * - Matrix (default is BLOSUM62) (-M in blastall) EXPECT
+    * - Expectation value (-e in blastall) NUM_OF_BITS
+    * - Number of bits to trigger gapping (-N in blastpgp) NCBI_GI
+      - If formated database use SeqIds in the NCBI format this option
+    * will turn printing of gis together with accessions. FILTER
+      - Multiple instances of values of this tag are concatenated and
+      passed to the engine as "filter_string" ("L" for low complexity
+      and "m" if filter should be set for lookup table only) - any
+      letter will turn default filtering on - DUST for nucleotides and
+    * SEG for proteins (-F in blastall) DESCRIPTIONS
+    * - Number of one-line descriptions in the output (-v in blastall)
+      ALIGNMENTS
+    * - Number of alignments to show (-b in blastall) COLOR_SCHEMA
+      - Color schema to use in printing of alternative alignment. This
+      option is valid only for blastp and blastn programs. If set - it
+    * will override option set by "ALIGNMENT_VIEW" TAX_BLAST
+      - Print taxonomy reports. This option is valid only for
+    * client/server version of regular Blast XML_OUTPUT
+      - Print XML Blast output. All other alignment view options will be
+    * disabled ENTREZ_QUERY
+      - Limit search to results of Entrez query. Only for client/server
+    * version RPSBLAST
+      - This tag with turn "blastp" or "blastx" search into RPS Blast
+    * search for the rps blast database. OOF_ALIGN
+      -This flag if set to non-zero digit will turn on OOF alignment for
+    * "blastx" and will set frame shift penalty to this value.
+      OTHER_ADVANCED
+      - this tag allows to input string analogous to the command line
+      parameters of blastall. Setting parameter in OTHER_ADVANCED tag
+      will override all other settings of this parameter. Supported
+      options include:
+          o -G
+          o gap open cost -E
+          o gap extend cost -q
+          o penalty for nucleotide mismatch -r
+          o reward for nucleotide match -e
+          o expect value -W
+          o wordsize -v
+          o Number of descriptions to print -b
+          o Number of alignments to show -K
+          o Number of best hits from a region to keep -Y
+    * effective search space ALIGNMENT_VIEW
+      - will set type of alignment to show. Available options include:
+          o 0 - Pairwise
+          o 1 - query-anchored with identities
+          o 2 - query-anchored without identities
+          o 3 - flat query-anchored with identities
+          o 4 - flat query-anchored without identities
+          o 7 - BLAST XML (equivalent to setting the XML_OUTPUT tag)
+    o 9 - Hit Table - to produce tabular output
+    * OVERVIEW
+    * - used to turn on or off printing of alignment overview image
+      BLAST_TYPE
+      - a special tag to distinguish different BLAST search types. See
+the description of a configuration file.
+
+
+      Server configuration file and logfile
+
+Default configuration file is "blast.rc" and logfile "wwwblast.log".
+Setting tag BLAST_TYPE to specific value may change these names.
+This is useful if few different search input pages use the same CGI
+search engine, but significantly different by content and priorities. A
+sample configuration file comes with this distribution:
+
+This file will set how many CPUs will be used in the BLAST search and
+what databases may be used with what programs. Logfile currently stores
+only limited information but also may be updated by programmers to store
+more values in it. Please note, that usually HTTPD servers run by
+accounts that do not have write access to disk, so the logfile
+permission should be set to 666.
+
+
+      How to debug WWW Blast programs
+
+There is a way to debug these programs.
+
+   1. Add line "setenv DEBUG_COMMAND_LINE TRUE" into the *.cgi file
+      (uncomment it)
+   2. Run search that results in the problem - this should create a file
+      "/tmp/__web.in" in the "/tmp" directory.
+   3. Set all necessary environment variables on the command line
+      (BLASTDB at least) and run from command-line: "blast.REAL <
+      /tmp/__web.in" 
+
+This should do your problematic search without WWW. If this resulted in
+coredump - you may look into the core file with:
+
+dbx blast.REAL core
+
+and then use command "where" to print stack.
+
+------------------------------------------------------------------------
+
+BLAST Help Desk <mailto:blast-help@ncbi.nlm.nih.gov>
+
+Last modified: Fri Jan 11, 2002
+
diff --git a/network/wwwblast/rpsblast.html b/network/wwwblast/rpsblast.html
new file mode 100644
index 00000000..60b3e6ce
--- /dev/null
+++ b/network/wwwblast/rpsblast.html
@@ -0,0 +1,211 @@
+<!--
+/* $Id: rpsblast.html,v 1.3 2003/06/24 21:53:54 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: rpsblast.html,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.3 $
+*
+* File Description:
+*         Template for standalone RPS BLAST Web page
+*
+* $Log: rpsblast.html,v $
+* Revision 1.3  2003/06/24 21:53:54  dondosha
+* Changed WWW_BLAST_TYPE to BLAST_TYPE
+*
+* Revision 1.2  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.1  2002/08/06 19:03:52  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/rpsblast.gif" ISMAP> 
+
+<FORM ACTION="blast.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<B>Choose program to use and database to search:</B>
+<P>
+<a href="docs/blast_program.html">Program</a>
+<select name = "PROGRAM">
+    <option VALUE = blastp> Protein vs. CDD 
+    <option VALUE = blastx> DNA vs. CDD 
+</select>
+<a href="docs/blast_databases.html">Database</a>
+<select name = "DATALIB">
+    <option VALUE = "CDD/test_CDD_db"> test_CDD_db 
+</select>
+
+<INPUT type="hidden" name = "BLAST_TYPE" value = "rpsblast">
+<INPUT TYPE = "hidden" NAME = "RPSBLAST">
+
+<!--
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+-->
+
+<P>
+Enter sequence below in <a href="docs/fasta.html">FASTA</a>  format 
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+<HR>
+
+The query sequence is 
+<a href="docs/filtered.html">filtered</a> 
+for low complexity regions by default.
+<BR>
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<a href="docs/matrix_info.html">Matrix</a>
+<select name = "MATRIX">
+    <option value = "PAM30"> PAM30 </option>
+    <option value = "PAM70"> PAM70 </option> 
+    <option value = "BLOSUM80"> BLOSUM80 </option>
+    <option selected value = "BLOSUM62"> BLOSUM62 </option>
+    <option value = "BLOSUM45"> BLOSUM45 </option>
+</select>
+<P>
+<a href="docs/newoptions.html#gencodes">Query Genetic Codes (Translated RPS Blast) 
+</a>
+<select name = "GENETIC_CODE">
+ <option> Standard (1) 
+ <option> Vertebrate Mitochondrial (2) 
+ <option> Yeast Mitochondrial (3) 
+ <option> Mold Mitochondrial; ... (4) 
+ <option> Invertebrate Mitochondrial (5) 
+ <option> Ciliate Nuclear; ... (6) 
+ <option> Echinoderm Mitochondrial (9) 
+ <option> Euplotid Nuclear (10) 
+ <option> Bacterial (11) 
+ <option> Alternative Yeast Nuclear (12) 
+ <option> Ascidian Mitochondrial (13) 
+ <option> Flatworm Mitochondrial (14) 
+ <option> Blepharisma Macronuclear (15) 
+</select>
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">
+<HR>
+<!--
+<INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp;
+-->
+<INPUT TYPE="checkbox" NAME="OVERVIEW"  CHECKED> 
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> query-anchored with identities
+    <option value=2> query-anchored without identities
+    <option value=3> flat query-anchored with identities
+    <option value=4> flat query-anchored without identities
+    <option value=7> BLAST XML
+    <option value=9> Hit Table 
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option selected> 100 
+    <option> 250 
+    <option> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option selected> 50 
+    <option> 100 
+    <option> 250 
+    <option> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/rpsblast.log b/network/wwwblast/rpsblast.log
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/network/wwwblast/rpsblast.log
diff --git a/network/wwwblast/rpsblast.rc b/network/wwwblast/rpsblast.rc
new file mode 100644
index 00000000..9ffb94ea
--- /dev/null
+++ b/network/wwwblast/rpsblast.rc
@@ -0,0 +1,30 @@
+# $Id: rpsblast.rc,v 1.2 2003/06/24 21:54:47 dondosha Exp $
+#
+#================================================================
+#
+#     This is dynamic configuration file for WWW BLAST service
+#              All lines started from '#' are ignored.
+#           "//" string considered as start of comments
+#
+#     Author Sergei B. Shavirin
+#
+# $Revision: 1.2 $
+#
+#
+##################################################################
+#
+#
+# Number of CPUs to use for a single request
+#
+# At this point this is irrelevant to RPS Blast... sorry..
+#
+NumCpuToUse     4
+#
+# Here are list of combinations program/database, 
+# that allowed by BLAST service. Format: <program> <db> <db> ...
+#
+# In RPS Blast regular protein search == "blastp" and translated RPS == "blastx"
+#
+blastp CDD/test_CDD_db
+blastx CDD/test_CDD_db
+
diff --git a/network/wwwblast/rpsblast_cs.html b/network/wwwblast/rpsblast_cs.html
new file mode 100644
index 00000000..651e44a1
--- /dev/null
+++ b/network/wwwblast/rpsblast_cs.html
@@ -0,0 +1,212 @@
+<!--
+/* $Id: rpsblast_cs.html,v 1.3 2003/06/24 21:53:54 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: rpsblast_cs.html,v $
+*
+* Author:  Sergei Shavirin
+*
+* Initial Version Creation Date: 03/14/2000
+*
+* $Revision: 1.3 $
+*
+* File Description:
+*         Template for standalone RPS BLAST Web page
+*
+* $Log: rpsblast_cs.html,v $
+* Revision 1.3  2003/06/24 21:53:54  dondosha
+* Changed WWW_BLAST_TYPE to BLAST_TYPE
+*
+* Revision 1.2  2003/05/22 16:20:45  dondosha
+* Removed references to blast_form.map: describe the map inside HTML
+*
+* Revision 1.1  2002/08/06 19:03:52  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<TITLE>BLAST Search </TITLE>
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<map name=img_map>
+<area shape=rect coords=2,1,48,21 href="http://www.ncbi.nlm.nih.gov">
+<area shape=rect coords=385,1,435,21 href="index.html">
+<area shape=rect coords=436,1,486,21 href="http://www.ncbi.nlm.nih.gov/Entrez/">
+<area shape=rect coords=487,1,508,21 href="docs/blast_help.html">
+</map>
+<img USEMAP=#img_map WIDTH=509 HEIGHT=22 SRC="images/rpsblast.gif" ISMAP> 
+
+<FORM ACTION="blast_cs.cgi" METHOD = POST NAME="MainBlastForm" ENCTYPE= "multipart/form-data">
+<B>Choose program to use and database to search:</B>
+<P>
+<a href="docs/blast_program.html">Program</a>
+<select name = "PROGRAM">
+    <option VALUE = blastp> Protein vs. CDD 
+    <option VALUE = blastx> DNA vs. CDD 
+</select>
+<a href="docs/blast_databases.html">Database</a>
+<select name = "DATALIB">
+    <option VALUE = "CDD/test_CDD_db"> test_CDD_db 
+</select>
+
+<INPUT type="hidden" name = "BLAST_TYPE" value = "rpsblast">
+<INPUT TYPE = "hidden" NAME = "RPSBLAST">
+
+<P>
+Enter here your input data as 
+<select name = "INPUT_TYPE"> 
+    <option> Sequence in FASTA format 
+    <option> Accession or GI 
+</select>
+<INPUT TYPE="submit" VALUE="Search">&nbsp;&nbsp;
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQUENCE.focus();">
+
+<BR>
+<textarea name="SEQUENCE" rows=6 cols=60>
+</textarea>
+<BR>
+Or load it from disk 
+<INPUT TYPE="file" NAME="SEQFILE">
+
+<P>Please read about <a href="/BLAST/fasta.html">FASTA</a> format description
+<HR>
+
+The query sequence is 
+<a href="/BLAST/filtered.html">filtered</a> 
+for low complexity regions by default.
+<BR>
+<a href="docs/newoptions.html#filter">Filter</a>
+ <INPUT TYPE="checkbox" VALUE="L" NAME="FILTER" CHECKED> Low complexity
+ <INPUT TYPE="checkbox" VALUE="m" NAME="FILTER"> Mask for lookup table only
+<P>
+<a href="docs/newoptions.html#expect">Expect</a>
+<select name = "EXPECT">
+    <option> 0.0001 
+    <option> 0.01 
+    <option> 1 
+    <option selected> 10 
+    <option> 100 
+    <option> 1000 
+</select>
+&nbsp;&nbsp;
+
+<a href="docs/matrix_info.html">Matrix</a>
+<select name = "MAT_PARAM">
+    <option value = "PAM30	 9	 1"> PAM30 </option>
+    <option value = "PAM70	 10	 1"> PAM70 </option> 
+    <option value = "BLOSUM80	 10	 1"> BLOSUM80 </option>
+    <option selected value = "BLOSUM62	 11	 1"> BLOSUM62 </option>
+    <option value = "BLOSUM45	 14	 2"> BLOSUM45 </option>
+</select>
+<P>
+<a href="docs/newoptions.html#gencodes">Query Genetic Codes (Translated RPS Blast) 
+</a>
+<select name = "GENETIC_CODE">
+ <option> Standard (1) 
+ <option> Vertebrate Mitochondrial (2) 
+ <option> Yeast Mitochondrial (3) 
+ <option> Mold Mitochondrial; ... (4) 
+ <option> Invertebrate Mitochondrial (5) 
+ <option> Ciliate Nuclear; ... (6) 
+ <option> Echinoderm Mitochondrial (9) 
+ <option> Euplotid Nuclear (10) 
+ <option> Bacterial (11) 
+ <option> Alternative Yeast Nuclear (12) 
+ <option> Ascidian Mitochondrial (13) 
+ <option> Flatworm Mitochondrial (14) 
+ <option> Blepharisma Macronuclear (15) 
+</select>
+<P>
+<a href="docs/full_options.html">Other advanced options:</a> 
+&nbsp;&nbsp;&nbsp;&nbsp; 
+<INPUT TYPE="text" NAME="OTHER_ADVANCED" VALUE="" MAXLENGTH="50">&nbsp;
+
+<!-- <INPUT TYPE="checkbox" NAME="TAX_BLAST"> Show <a href ="docs/taxblasthelp.html">Tax Blast reports</a> -->
+
+<HR>
+
+<!-- <INPUT TYPE="checkbox" NAME="NCBI_GI" >&nbsp;&nbsp;
+<a href="docs/newoptions.html#ncbi-gi"> NCBI-gi</a>
+&nbsp;&nbsp;&nbsp;&nbsp; -->
+
+<INPUT TYPE="checkbox" NAME="OVERVIEW"  CHECKED> 
+
+<a href="docs/newoptions.html#graphical-overview">Graphical Overview</a>
+&nbsp;&nbsp;
+<a href="docs/options.html#alignmentviews">Alignment view</a>
+<select name = "ALIGNMENT_VIEW">
+    <option value=0> Pairwise
+    <option value=1> query-anchored with identities
+    <option value=2> query-anchored without identities
+    <option value=3> flat query-anchored with identities
+    <option value=4> flat query-anchored without identities
+    <option value=7> BLAST XML
+    <option value=9> Hit Table
+</select>
+<BR>
+<a href="docs/newoptions.html#descriptions">Descriptions</a>
+<select name = "DESCRIPTIONS">
+    <option> 0 
+    <option> 10 
+    <option> 50 
+    <option selected> 100 
+    <option> 250 
+    <option> 500 
+</select>
+&nbsp;&nbsp;
+<a href="docs/newoptions.html#alignments">Alignments</a>
+<select name = "ALIGNMENTS">
+    <option> 0 
+    <option> 10 
+    <option selected> 50 
+    <option> 100 
+    <option> 250 
+    <option> 500 
+</select>
+<a href="docs/color_schema.html">Color schema</a>
+<select name = "COLOR_SCHEMA">
+    <option selected value = 0> No color schema 
+    <option value = 1> Color schema 1 
+    <option value = 2> Color schema 2  
+    <option value = 3> Color schema 3 
+    <option value = 4> Color schema 4 
+    <option value = 5> Color schema 5 
+    <option value = 6> Color schema 6 
+</select>
+<P>
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="MainBlastForm.SEQUENCE.value='';MainBlastForm.SEQFILE.value='';MainBlastForm.SEQUENCE.focus();">
+<INPUT TYPE="submit" VALUE="Search">
+</FORM>
+<HR>
+<ADDRESS>
+Comments and suggestions to:&lt; <a href="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</a> &gt
+</ADDRESS>
+<BR>
+<!-- Created: Thu Mar 16 16:41:05 EST 2000 -->
+<!-- hhmts start -->
+Last modified: Jan 11, 2002
+<!-- hhmts end -->
+</BODY>
+</HTML>
diff --git a/network/wwwblast/wblast2.cgi b/network/wwwblast/wblast2.cgi
new file mode 100755
index 00000000..a08ae344
--- /dev/null
+++ b/network/wwwblast/wblast2.cgi
@@ -0,0 +1,13 @@
+#!/bin/csh -f
+
+#
+# $Id: wblast2.cgi,v 1.1 2002/08/06 19:03:52 dondosha Exp $
+#
+
+echo "Content-type: text/html"
+echo ""
+
+#setenv DEBUG_COMMAND_LINE TRUE
+setenv BLASTDB db
+
+./wblast2.REAL
diff --git a/network/wwwblast/wblast2.html b/network/wwwblast/wblast2.html
new file mode 100644
index 00000000..8cf1b8a2
--- /dev/null
+++ b/network/wwwblast/wblast2.html
@@ -0,0 +1,283 @@
+<!--
+/* $Id: wblast2.html,v 1.2 2003/07/14 19:49:02 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: wblast2.html,v $
+*
+* Initial Version Creation Date: 11/02/2000
+*
+* $Revision: 1.2 $
+*
+* Authors: Ilya Dondoshansky, Sergey Shavirin
+*
+* File Description:
+*         Template for standalone BLAST 2 sequences Web page
+*
+* $Log: wblast2.html,v $
+* Revision 1.2  2003/07/14 19:49:02  dondosha
+* Some improvements in javascript
+*
+* Revision 1.1  2002/08/06 19:03:52  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<HEAD>
+<title>Blast 2 Sequences</title>
+<SCRIPT LANGUAGE="Javascript">
+
+<!-- HIDE
+function chan(a)
+{
+alert(a);
+	if (a.value == 'off') {
+		document.bl2.gopen.value=11;
+		document.bl2.gext.value=1;
+		document.bl2.match.value="";
+		document.bl2.msmatch.value="";
+		a.value = 'on';
+	} else {
+		document.bl2.gopen.value=5;
+		document.bl2.gext.value=2;
+		document.bl2.match.value="1";
+		document.bl2.msmatch.value="-2";
+		a.value = 'off';
+	}
+}
+
+function chan_prog(a)
+{
+	if (a.selectedIndex == 0) {
+		document.bl2.gopen.value = 5;
+		document.bl2.gext.value = 2;
+		document.bl2.match.value="1"; 
+		document.bl2.msmatch.value="-2";
+		document.bl2.word.value="11";
+                document.bl2.matrix.options.length = 1;
+                document.bl2.matrix.options[0] = null;
+                document.bl2.matrix.options[0] = new Option('Not Applicable');
+                document.bl2.matrix.options[0].text='Not Applicable';
+		document.bl2.matrix.options[0].value=-1;
+		document.bl2.strand.options.length = 4;
+		document.bl2.strand.options[0] = null;
+		document.bl2.strand.options[0] = new Option('Both strands');
+             document.bl2.strand.options[0].text='Both strands';
+             document.bl2.strand.options[0].value=3;
+             document.bl2.strand.options[0].selected = true;
+             document.bl2.strand.options[1].text='Top strand';
+             document.bl2.strand.options[1].value=1;
+             document.bl2.strand.options[2].text='Reverse strand';
+             document.bl2.strand.options[2].value=2;
+	} else if (a.selectedIndex >= 1) {
+                document.bl2.matrix.options.length = 7;
+	        document.bl2.matrix.options[0] = null;
+        	document.bl2.matrix.options[0] = new Option('BLOSUM62');
+             document.bl2.matrix.options[0].text='BLOSUM62';
+             document.bl2.matrix.options[0].value=0;
+             document.bl2.matrix.options[0].selected = true;
+             document.bl2.matrix.options[1].text='PAM30';
+             document.bl2.matrix.options[1].value=1;
+             document.bl2.matrix.options[2].text='PAM70';
+             document.bl2.matrix.options[2].value=2;
+             document.bl2.matrix.options[3].text='PAM250';
+             document.bl2.matrix.options[3].value=3;
+             document.bl2.matrix.options[4].text='BLOSUM90';
+             document.bl2.matrix.options[4].value=4;
+             document.bl2.matrix.options[5].text='BLOSUM50';
+             document.bl2.matrix.options[5].value=5;
+		document.bl2.word.value="3";
+		if (document.bl2.matrix.selectedIndex == 0) {
+			document.bl2.gopen.value = 11;
+			document.bl2.gext.value = 1;
+		} else if (document.bl2.matrix.selectedIndex == 1) {
+			document.bl2.gopen.value = 9;
+			document.bl2.gext.value = 1;
+		} else if (document.bl2.matrix.selectedIndex == 2) {
+			document.bl2.gopen.value = 10;
+			document.bl2.gext.value = 1;
+		} else if (document.bl2.matrix.selectedIndex == 3) {
+			document.bl2.gopen.value = 14;
+			document.bl2.gext.value = 2;
+		} else if (document.bl2.matrix.selectedIndex == 4) {
+			document.bl2.gopen.value = 10;
+			document.bl2.gext.value = 1;
+		} else if (document.bl2.matrix.selectedIndex == 5) {
+			document.bl2.gopen.value = 13;
+			document.bl2.gext.value = 2;
+		}
+		document.bl2.match.value="";
+		document.bl2.msmatch.value="";
+                document.bl2.megablast.checked = 0;
+             	document.bl2.strand.options.length = 1;
+	        document.bl2.strand.options[0] = null;
+       	     	document.bl2.strand.options[0] = new Option('Not Applicable');
+             	document.bl2.strand.options[0].selected = true;
+             document.bl2.strand.options[0].text='Not Applicable';
+             document.bl2.strand.options[0].value=0;
+	}
+}
+
+function update_mtrx(a)
+{
+	if (document.bl2.program.selectedIndex == 0) {
+		return;
+	}
+		document.bl2.word.value = 3;
+	if (a.selectedIndex == 0) {   /* BLOSUM62 */
+		document.bl2.gopen.value = 11;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 1) {  /* PAM30 */
+		document.bl2.gopen.value = 9;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 2) {  /* PAM70 */
+		document.bl2.gopen.value = 10;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 3) {  /* PAM250 */
+		document.bl2.gopen.value = 14;
+		document.bl2.gext.value = 2;
+	} else if (a.selectedIndex == 4) {  /* BLOSUM90 */
+		document.bl2.gopen.value = 10;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 5) {   /* BLOSUM50 */
+		document.bl2.gopen.value = 13;
+		document.bl2.gext.value = 2;
+	}
+}
+function clear_sequence() {
+      document.bl2.seqfile1.value='';
+      document.bl2.seqfile2.value='';
+      document.bl2.sseq.value='';
+      document.bl2.seq.value='';
+      document.bl2.one.value='';
+      document.bl2.two.value='';
+      document.bl2.to.value='';
+      document.bl2.tto.value='';
+      document.bl2.from.value='';
+      document.bl2.ffrom.value='';
+      document.bl2.seq.focus();
+}
+
+function megablast_update(a)
+{
+        if (a.checked == 0) {
+         document.bl2.word.value = 11;
+         document.bl2.gopen.value = 5;
+         document.bl2.gext.value = 2;
+        } else {
+         if (document.bl2.program.selectedIndex != 0) {
+            document.bl2.program.selectedIndex = 0;
+            chan_prog(document.bl2.program);
+         }
+         document.bl2.word.value = 28;
+         document.bl2.gopen.value = "";
+         document.bl2.gext.value = "";
+     }
+}
+
+// -->
+
+</SCRIPT>
+</HEAD>
+
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<A HREF="blast_form.map">
+<IMG SRC="images/bl2seq.gif" BORDER=0 ISMAP></A>
+
+<FORM NAME="bl2" method="Post" action="wblast2.cgi?0" enctype="multipart/form-data">
+This tool produces the alignment of two given sequences using BLAST<BR>
+engine for local alignment. 
+<P>
+<A HREF=docs/blast_program.html>Program</A>
+<select name="program" onChange="chan_prog(this)">
+<option selected> blastn
+<option> blastp
+<option> tblastn
+<option> blastx
+<option> tblastx
+</select>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+<INPUT TYPE="submit" VALUE="Align">
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="clear_sequence()">
+<HR>
+<font color=ff0000>Sequence 1: </font>&nbsp;&nbsp;&nbsp;&nbsp;
+from: <INPUT type=text size=8 name="from"> &nbsp;&nbsp; to: 
+<INPUT type=text size=8 name="to">
+<BR>
+Enter sequence in FASTA format 
+<BR>
+<textarea name="seq" rows=6 cols=60></textarea><BR>
+or download from file <INPUT type=file name="seqfile1">
+<P>
+<HR>
+<font color=ff0000>Sequence 2: </font>&nbsp;&nbsp;&nbsp;&nbsp; 
+from:<INPUT type=text size=8 name="ffrom"> &nbsp;&nbsp; to: 
+<INPUT type=text size=8 name="tto">
+<BR>
+Enter sequence in FASTA format
+<BR>
+<textarea name="sseq" rows=6 cols=60></textarea>
+<BR>
+or download from file <INPUT type=file name="seqfile2">
+<HR>
+Parameters used in <A HREF=docs/full_options.html#blastn>BLASTN </A>program only:<BR>
+<strong>Reward for a match:</strong><INPUT type=text size=8 name="match" value=1>
+<strong>Penalty for a mismatch:</strong><INPUT type=text size=8 name="msmatch" value=-2>
+<HR> 
+<A HREF=docs/options.html#matrix>Matrix</A>
+<select name="matrix" onChange="update_mtrx(this)">
+<option> Not Applicable
+<!-- <option> 0 BLOSUM62
+<option> 1 PAM30
+<option> 2 PAM70
+<option> 3 PAM250
+<option> 4 BLOSUM90
+<option> 5 BLOSUM50
+// -->
+</select>
+Open gap 
+<INPUT type=text size=4 name="gopen" value=5>
+and extension gap
+<INPUT type=text size=4 name="gext" value=2> penalties
+<BR>
+Gap x_dropoff <INPUT type=text size=4 name="dropoff" value=50>
+<A HREF=docs/newoptions.html#expect>Expect value</A> 
+<INPUT type=text size=4 name="expect" value=10> 
+Word size <INPUT type=text size=4 name="word" value=11>
+<a href="docs/newoptions.html#filter">Filter</a>
+<INPUT TYPE="checkbox" NAME="Filter" VALUE="1" CHECKED>
+<HR>
+<INPUT TYPE="submit" VALUE="Align">
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="clear_sequence()">
+<INPUT TYPE="reset" VALUE="Reset form">
+</form>
+<HR>
+<ADDRESS> Comments and suggetstions to: 
+<A HREF="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</A>
+<BR>
+</body>
+</html>
diff --git a/network/wwwblast/wblast2_cs.cgi b/network/wwwblast/wblast2_cs.cgi
new file mode 100755
index 00000000..dca0ce8c
--- /dev/null
+++ b/network/wwwblast/wblast2_cs.cgi
@@ -0,0 +1,13 @@
+#!/bin/csh -f
+
+#
+# $Id: wblast2_cs.cgi,v 1.1 2002/08/06 19:03:52 dondosha Exp $
+#
+
+echo "Content-type: text/html"
+echo ""
+
+#setenv DEBUG_COMMAND_LINE TRUE
+setenv BLASTDB db
+
+./wblast2_cs.REAL
diff --git a/network/wwwblast/wblast2_cs.html b/network/wwwblast/wblast2_cs.html
new file mode 100644
index 00000000..32deb922
--- /dev/null
+++ b/network/wwwblast/wblast2_cs.html
@@ -0,0 +1,235 @@
+<!--
+/* $Id: wblast2_cs.html,v 1.1 2002/08/06 19:03:53 dondosha Exp $
+* ===========================================================================
+*
+*                            PUBLIC DOMAIN NOTICE
+*               National Center for Biotechnology Information
+*
+*  This software/database is a "United States Government Work" under the
+*  terms of the United States Copyright Act.  It was written as part of
+*  the author's official duties as a United States Government employee and
+*  thus cannot be copyrighted.  This software/database is freely available
+*  to the public for use. The National Library of Medicine and the U.S.
+*  Government have not placed any restriction on its use or reproduction.
+*
+*  Although all reasonable efforts have been taken to ensure the accuracy
+*  and reliability of the software and data, the NLM and the U.S.
+*  Government do not and cannot warrant the performance or results that
+*  may be obtained by using this software or data. The NLM and the U.S.
+*  Government disclaim all warranties, express or implied, including
+*  warranties of performance, merchantability or fitness for any particular
+*  purpose.
+*
+*  Please cite the author in any work or product based on this material.
+*
+* ===========================================================================
+*
+* File Name:  $RCSfile: wblast2_cs.html,v $
+*
+* Initial Version Creation Date: 11/02/2000
+*
+* $Revision: 1.1 $
+*
+* Authors: Ilya Dondoshansky, Sergey Shavirin
+*
+* File Description:
+*         Template for standalone BLAST 2 sequences Web page
+*
+* $Log: wblast2_cs.html,v $
+* Revision 1.1  2002/08/06 19:03:53  dondosha
+* WWW BLAST server, initial CVS revision
+*
+
+-->
+<HTML>
+<HEAD>
+<title>Blast 2 Sequences</title>
+<SCRIPT LANGUAGE="Javascript">
+
+<!-- HIDE
+function chan(a)
+{
+alert(a);
+	if (a.value == 'off') {
+		document.bl2.gopen.value=11;
+		document.bl2.gext.value=1;
+		document.bl2.match.value="";
+		document.bl2.msmatch.value="";
+		a.value = 'on';
+	} else {
+		document.bl2.gopen.value=5;
+		document.bl2.gext.value=2;
+		document.bl2.match.value="1";
+		document.bl2.msmatch.value="-2";
+		a.value = 'off';
+	}
+}
+
+function chan_prog(a)
+{
+	if (a.selectedIndex == 0) {
+		document.bl2.gopen.value = 5;
+		document.bl2.gext.value = 2;
+		document.bl2.match.value="1"; 
+		document.bl2.msmatch.value="-2";
+		document.bl2.word.value="11";
+                document.bl2.matrix.options.length = 1;
+                document.bl2.matrix.options[0].text='Not Applicable';
+	} else if (a.selectedIndex >= 1) {
+                document.bl2.matrix.options.length = 6;
+                document.bl2.matrix.options[0].text='BLOSUM62';
+                document.bl2.matrix.options[1].text='PAM30';
+                document.bl2.matrix.options[2].text='PAM70';
+                document.bl2.matrix.options[3].text='PAM250';
+                document.bl2.matrix.options[4].text='BLOSUM90';
+                document.bl2.matrix.options[5].text='BLOSUM50';
+		document.bl2.word.value="3";
+		if (document.bl2.matrix.selectedIndex == 0) {
+			document.bl2.gopen.value = 11;
+			document.bl2.gext.value = 1;
+		} else if (document.bl2.matrix.selectedIndex == 1) {
+			document.bl2.gopen.value = 9;
+			document.bl2.gext.value = 1;
+	} else if (document.bl2.matrix.selectedIndex == 2) {
+			document.bl2.gopen.value = 10;
+			document.bl2.gext.value = 1;
+	} else if (document.bl2.matrix.selectedIndex == 3) {
+			document.bl2.gopen.value = 14;
+			document.bl2.gext.value = 2;
+	} else if (document.bl2.matrix.selectedIndex == 4) {
+			document.bl2.gopen.value = 10;
+			document.bl2.gext.value = 1;
+	} else if (document.bl2.matrix.selectedIndex == 5) {
+			document.bl2.gopen.value = 13;
+			document.bl2.gext.value = 2;
+	}
+		document.bl2.match.value="";
+		document.bl2.msmatch.value="";
+	}
+}
+
+function update_mtrx(a)
+{
+	if (document.bl2.program.selectedIndex == 0) {
+		return;
+	}
+		document.bl2.word.value = 3;
+	if (a.selectedIndex == 0) {   /* BLOSUM62 */
+		document.bl2.gopen.value = 11;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 1) {  /* PAM30 */
+		document.bl2.gopen.value = 9;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 2) {  /* PAM70 */
+		document.bl2.gopen.value = 10;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 3) {  /* PAM250 */
+		document.bl2.gopen.value = 14;
+		document.bl2.gext.value = 2;
+	} else if (a.selectedIndex == 4) {  /* BLOSUM90 */
+		document.bl2.gopen.value = 10;
+		document.bl2.gext.value = 1;
+	} else if (a.selectedIndex == 5) {   /* BLOSUM50 */
+		document.bl2.gopen.value = 13;
+		document.bl2.gext.value = 2;
+	}
+}
+function clear_sequence() {
+      document.bl2.seqfile1.value='';
+      document.bl2.seqfile2.value='';
+      document.bl2.sseq.value='';
+      document.bl2.seq.value='';
+      document.bl2.one.value='';
+      document.bl2.two.value='';
+      document.bl2.to.value='';
+      document.bl2.tto.value='';
+      document.bl2.from.value='';
+      document.bl2.ffrom.value='';
+      document.bl2.seq.focus();
+}
+// -->
+
+</SCRIPT>
+</HEAD>
+
+<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
+<A HREF="blast_form.map">
+<IMG SRC="images/bl2seq.gif" BORDER=0 ISMAP></A>
+
+<FORM NAME="bl2" method="Post" action="wblast2_cs.cgi" enctype="multipart/form-data">
+This tool produces the alignment of two given sequences using BLAST<BR>
+engine for local alignment. 
+<P>
+<A HREF=docs/blast_program.html>Program</A>
+<select name="program" onChange="chan_prog(this)">
+<option selected> blastn
+<option> blastp
+<option> tblastn
+<option> blastx
+<option> tblastx
+</select>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+<INPUT TYPE="submit" VALUE="Align">
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="clear_sequence()">
+<HR>
+<font color=ff0000>Sequence 1: </font>&nbsp;&nbsp;&nbsp;&nbsp;
+from: <INPUT type=text size=8 name="from"> &nbsp;&nbsp; to: 
+<INPUT type=text size=8 name="to">
+<BR>
+Enter accession or GI <INPUT type=text size=8 name="one"> 
+or sequence in FASTA format 
+<BR>
+<textarea name="seq" rows=6 cols=60></textarea><BR>
+or download from file <INPUT type=file name="seqfile1">
+<P>
+<HR>
+<font color=ff0000>Sequence 2: </font>&nbsp;&nbsp;&nbsp;&nbsp; 
+from:<INPUT type=text size=8 name="ffrom"> &nbsp;&nbsp; to: 
+<INPUT type=text size=8 name="tto">
+<BR>
+Enter accession or GI <INPUT type=text size=8 name="two">
+or sequence in FASTA format
+<BR>
+<textarea name="sseq" rows=6 cols=60></textarea>
+<BR>
+or download from file <INPUT type=file name="seqfile2">
+<HR>
+Parameters used in <A HREF=docs/full_options.html#blastn>BLASTN </A>program only:<BR>
+<strong>Reward for a match:</strong><INPUT type=text size=8 name="match" value=1>
+<strong>Penalty for a mismatch:</strong><INPUT type=text size=8 name="msmatch" value=-2>
+<HR>
+<A HREF=docs/options.html#matrix>Matrix</A>
+<select name="matrix" onChange="update_mtrx(this)">
+<option> Not Applicable
+<!-- <option> 0 BLOSUM62
+<option> 1 PAM30
+<option> 2 PAM70
+<option> 3 PAM250
+<option> 4 BLOSUM90
+<option> 5 BLOSUM50
+// -->
+</select>
+Open gap 
+<INPUT type=text size=4 name="gopen" value=5>
+and extension gap
+<INPUT type=text size=4 name="gext" value=2> penalties
+<BR>
+Gap x_dropoff <INPUT type=text size=4 name="dropoff" value=50>
+<A HREF=docs/newoptions.html#expect>Expect value</A> 
+<INPUT type=text size=4 name="expect" value=10> 
+Word size <INPUT type=text size=4 name="word" value=11>
+<a href="docs/newoptions.html#filter">Filter</a>
+<INPUT TYPE="checkbox" NAME="Filter" VALUE="1" CHECKED>
+<HR>
+<INPUT TYPE="submit" VALUE="Align">
+<INPUT TYPE="button" VALUE="Clear sequence" onClick="clear_sequence()">
+<INPUT TYPE="reset" VALUE="Reset form">
+</form>
+<HR>
+<ADDRESS> Comments and suggetstions to: 
+<A HREF="mailto:blast-help@ncbi.nlm.nih.gov">blast-help@ncbi.nlm.nih.gov</A>
+<BR>
+</body>
+</html>
diff --git a/network/wwwblast/wwwblast.log b/network/wwwblast/wwwblast.log
new file mode 100644
index 00000000..e69de29b
--- /dev/null
+++ b/network/wwwblast/wwwblast.log