path: root/doc/man/blast.1

.TH BLAST 1 2003-04-27 NCBI "NCBI Tools User's Manual"
.SH NAME
bl2seq, blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop \- Basic Local Alignment Search Tool
.SH SYNOPSIS
.B bl2seq
[\|\fB\-\fP\|]
[\|\fB\-A\fP\|]
[\|\fB\-D\fP\ \fIN\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-I\fP\ \fIstr\fP\|]
[\|\fB\-J\fP\ \fIstr\fP\|]
[\|\fB\-M\fP\ \fIstr\fP\|]
[\|\fB\-S\fP\ \fIN\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-W\fP\ \fIN\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-Y\fP\ \fIX\fP\|]
[\|\fB\-a\fP\ \fIfilename\fP\|]
[\|\fB\-d\fP\ \fIN\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-g\ F\fP\|]
\fB\-i\fP\ \fIfilename\fP
\fB\-j\fP\ \fIfilename\fP
[\|\fB\-m\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
\fB\-p\fP\ \fIstr\fP
[\|\fB\-q\fP\ \fIN\fP\|]
[\|\fB\-r\fP\ \fIN\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
.PP
.B blastall
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIN\fP\|]
[\|\fB\-B\fP\ \fIN\fP\|]
[\|\fB\-D\fP\ \fIN\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-K\fP\ \fIN\fP\|]
[\|\fB\-L\fP\ \fIstart,stop\fP\|]
[\|\fB\-M\fP\ \fIstr\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-P\fP\ \fIN\fP\|]
[\|\fB\-Q\fP\ \fIN\fP\|]
[\|\fB\-R\fP\ \fIfilename\fP\|]
[\|\fB\-S\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-W\fP\ \fIN\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-Y\fP\ \fIX\fP\|]
[\|\fB\-Z\fP\ \fIN\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-f\fP\ \fIN\fP\|]
[\|\fB\-g\ F\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-l\fP\ \fIstr\fP\|]
[\|\fB\-m\fP\ \fIN\fP\|]
[\|\fB\-n\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
\fB\-p\fP\ \fIstr\fP
[\|\fB\-q\fP\ \fIN\fP\|]
[\|\fB\-r\fP\ \fIN\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-w\fP\ \fIN\fP\|]
[\|\fB\-y\fP\ \fIX\fP\|]
[\|\fB\-z\fP\ \fIX\fP\|]
.PP
.B blastcl3
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIN\fP\|]
[\|\fB\-B\fP\ \fIN\fP\|]
[\|\fB\-D\fP\ \fIN\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-K\fP\ \fIN\fP\|]
[\|\fB\-L\fP\ \fIstart,stop\fP\|]
[\|\fB\-M\fP\ \fIstr\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-Q\fP\ \fIN\fP\|]
[\|\fB\-R\fP\|]
[\|\fB\-S\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-W\fP\ \fIN\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-Y\fP\ \fIX\fP\|]
[\|\fB\-Z\fP\ \fIN\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-f\fP\ \fIN\fP\|]
[\|\fB\-g\ F\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-m\fP\ \fIN\fP\|]
[\|\fB\-n\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
\fB\-p\fP\ \fIstr\fP
[\|\fB\-q\fP\ \fIN\fP\|]
[\|\fB\-r\fP\ \fIN\fP\|]
[\|\fB\-u\fP\ \fIstr\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-w\fP\ \fIN\fP\|]
[\|\fB\-y\fP\ \fIX\fP\|]
[\|\fB\-z\fP\ \fIX\fP\|]
.PP
.B blastpgp
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIN\fP\|]
[\|\fB\-B\fP\ \fIfilename\fP\|]
[\|\fB\-C\fP\ \fIfilename\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F T\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-H\fP\ \fIN\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-K\fP\ \fIN\fP\|]
[\|\fB\-L\fP\ \fIN\fP\|]
[\|\fB\-M\fP\ \fIstr\fP\|]
[\|\fB\-N\fP\ \fIX\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-P\fP\ \fIN\fP\|]
[\|\fB\-Q\fP\ \fIfilename\fP\|]
[\|\fB\-R\fP\ \fIfilename\fP\|]
[\|\fB\-S\fP\ \fIN\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-W\fP\ \fIN\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-Y\fP\ \fIX\fP\|]
[\|\fB\-Z\fP\ \fIN\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
[\|\fB\-c\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-f\fP\ \fIN\fP\|]
[\|\fB\-g\ F\fP\|]
[\|\fB\-h\fP\ \fIX\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-j\fP\ \fIN\fP\|]
[\|\fB\-k\fP\ \fIfilename\fP\|]
[\|\fB\-l\fP\ \fIstr\fP\|]
[\|\fB\-m\fP\ \fIN\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIstr\fP\|]
[\|\fB\-s\fP\|]
[\|\fB\-t\ F\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-y\fP\ \fIX\fP\|]
[\|\fB\-z\fP\ \fIN\fP\|]
.PP
.B impala
[\|\fB\-\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-H\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-M\fP\ \fIstr\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-P\fP\ \fIfilename\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
[\|\fB\-c\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-h\fP\ \fIX\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-j\fP\ \fIN\fP\|]
[\|\fB\-m\fP\ \fIN\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-y\fP\ \fIX\fP\|]
[\|\fB\-z\fP\ \fIN\fP\|]
.PP
.B megablast
[\|\fB\-\fP\|]
[\|\fB\-A\fP\ \fIN\fP\|]
[\|\fB\-D\fP\ \fIN\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-H\fP\ \fIN\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-L\fP\ \fIstart,stop\fP\|]
[\|\fB\-M\fP\ \fIN\fP\|]
[\|\fB\-N\fP\ \fIN\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-P\fP\ \fIN\fP\|]
[\|\fB\-Q\fP\ \fIfilename\fP\|]
[\|\fB\-R\fP\|]
[\|\fB\-S\fP\ \fIN\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-W\fP\ \fIN\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-Z\fP\ \fIN\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-f\fP\|]
[\|\fB\-g\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-l\fP\ \fIstr\fP\|]
[\|\fB\-m\fP\ \fIN\fP\|]
[\|\fB\-n\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIX\fP\|]
[\|\fB\-q\fP\ \fIN\fP\|]
[\|\fB\-r\fP\ \fIN\fP\|]
[\|\fB\-t\fP\ \fIN\fP\|]
[\|\fB\-s\fP\ \fIN\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-y\fP\ \fIN\fP\|]
[\|\fB\-z\fP\ \fIX\fP\|]
.PP
.B rpsblast
[\|\fB\-\fP\|]
[\|\fB\-F\fP\ \fIstr\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-L\fP\ \fIstart,stop\fP\|]
[\|\fB\-N\fP\ \fIX\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-P\fP\ \fIN\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-U\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-Y\fP\ \fIX\fP\|]
[\|\fB\-Z\fP\ \fIN\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
\fB\-d\fP\ \fIfilename\fP
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-g\ F\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-l\fP\ \fIfilename\fP\|]
[\|\fB\-m\fP\ \fIN\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\ F\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
[\|\fB\-y\fP\ \fIX\fP\|]
[\|\fB\-z\fP\ \fIN\fP\|]
.PP
.B seedtop
[\|\fB\-\fP\|]
[\|\fB\-C\fP\ \fIN\fP\|]
[\|\fB\-D\fP\ \fIN\fP\|]
[\|\fB\-E\fP\ \fIN\fP\|]
[\|\fB\-F\fP\|]
[\|\fB\-G\fP\ \fIN\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-J\fP\|]
[\|\fB\-M\fP\ \fIstr\fP\|]
[\|\fB\-O\fP\ \fIfilename\fP\|]
[\|\fB\-S\fP\ \fIN\fP\|]
[\|\fB\-X\fP\ \fIN\fP\|]
[\|\fB\-b\fP\ \fIN\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-e\fP\ \fIX\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-k\fP\ \fIfilename\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIstr\fP\|]
[\|\fB\-q\fP\ \fIN\fP\|]
[\|\fB\-r\fP\ \fIN\fP\|]
[\|\fB\-v\fP\ \fIN\fP\|]
.SH DESCRIPTION
This manual page documents briefly the commands \fBbl2seq\fP,
\fBblastall\fP, \fBblastcl3\fP, \fBblastpgp\fP, \fBimpala\fP,
\fBmegablast\fP, \fBrpsblast\fP, and \fBseedtop\fP.  These commands
are documented together because they have a lot of common options.
.PP
\fBbl2seq\fP performs a comparison between two sequences using either
the blastn or blastp algorithm.  Both sequences must be either
nucleotides or proteins.
.PP
\fBblastall\fP finds the best matches in a local database for a sequence.
.PP
\fBblastcl3\fP accesses the newest NCBI BLAST search engine (version
2.0).  The software behind BLAST version 2.0 was written from scratch
to allow BLAST to handle the new challenges posed by the sequence
databases in the coming years.  Updates to this software will continue
in the coming years.
.PP
\fBblastpgp\fP performs gapped blastp searches and can be used to
perform iterative searches in psi-blast and phi-blast mode.
.PP
\fBimpala\fP searches a database of score matrices, prepared by
\fBcopymat\fP(1), producing BLAST-like output.
.PP
\fBmegablast\fP uses the greedy algorithm of Webb Miller et al. for
nucleotide sequence alignment search and concatenates many queries to
save time spent scanning the database. This program is optimized for
aligning sequences that differ slightly as a result of sequencing or
other similar "errors". It is up to 10 times faster than more common
sequence similarity programs and therefore can be used to swiftly
compare two large sets of sequences against each other.
.PP
\fBrpsblast\fP (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'.
\fBrpsblast\fP 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.
.PP
\fBseedtop\fP answers two relatively simple questions:
.PD 0
.IP 1.
Given a sequence and a database of patterns, which patterns occur
in the sequence and where?
.IP 2.
Given a pattern and a sequence database, which sequences contain the
pattern and where?
.PD
.PP
Some of these commands support multiple types of comparison, governed
by the \fB\-p\fP ("program") flag:
.IP blastp 12
compares an amino acid query sequence against a protein sequence
database.
.IP blastn 12
compares a nucleotide query sequence against a nucleotide sequence
database.
.IP blastx 12
compares the six-frame conceptual translation products of a nucleotide
query sequence (both strands) against a protein sequence database.
For \fBbl2seq\fP, the nucleotide should be the first sequence given.
.IP psitblastn 12
compares a protein query sequence against a nucleotide sequence
database dynamically translated in all six reading frames (both
strands) using a position specific matrix created by PSI-BLAST.
.IP tblastn 12
compares a protein query sequence against a nucleotide sequence
database dynamically translated in all six reading frames (both
strands).  For \fBbl2seq\fP, the nucleotide should be the second
sequence given.
.IP tblastx 12
compares the six-frame translations of a nucleotide query sequence
against the six-frame translations of a nucleotide sequence database.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-A\fP (bl2seq)
Input sequences in the form of accession.version
.TP
\fB\-A\fP\ \fIN\fP (blastall, blastcl3, blastpgp, megablast) Multiple
Hits window size (default is 40 for blastpgp and 0 for other command,
but blastall and blastcl3 interpret 0 as 40 for all programs but blastn
and megablast)
.TP
\fB\-B\fP\ \fIN\fP (blastall, blastcl3)
Number of concatenated queries, in blastn or tblastn mode
.TP
\fB\-B\fP\ \fIfilename\fP (blastpgp)
Input Alignment File for PSI-BLAST Restart
.TP
\fB\-C\fP\ \fIfilename\fP (blastpgp)
Output File for PSI-BLAST Checkpointing
.TP
\fB\-C\fP\ \fIN\fP (seedtop)
Score only or not (default = 1)
.TP
\fB\-D\fP\ \fIN\fP (bl2seq)
Output format:
.RS
.PD 0
.IP 0
traditional (default)
.IP 1
tabular
.PD
.RE
.TP
\fB\-D\fP\ \fIN\fP (blastall, blastcl3)
Translate sequences in the database according to genetic code \fIN\fP
in /usr/share/ncbi/data/gc.prt (default is 1; only applies to tblast*)
.TP
\fB\-D\fP\ \fIN\fP (megablast)
Type of output:
.RS
.PD 0
.IP 0
alignment endpoints and score (default)
.IP 1
all ungapped segments endpoints,
.IP 2
traditional BLAST output,
.IP 3
tab-delimited one line format
.PD
.RE
.TP
\fB\-D\fP\ \fIN\fP (seedtop)
Cost decline to align (default = 99999)
.TP
\fB\-E\fP\ \fIN\fP (bl2seq)
Extending a gap costs \fIN\fP (-1 invokes default behavior; anything
else can result in unreliable statistics)
.TP
\fB\-E\fP\ \fIN\fP (blastall, blastcl3, megablast)
Extending a gap costs \fIN\fP (zero invokes default behavior)
.TP
\fB\-E\fP\ \fIN\fP (blastpgp, impala, seedtop)
Extending a gap costs \fIN\fP (default is 1)
.TP
\fB\-F\fP\ \fIstr\fP (bl2seq, blastall, blastpgp, blastcl3, impala,
megablast, rpsblast)
Filter options for DUST or SEG; defaults to \fBT\fP for bl2seq,
blastall, blastcl3, and megablast, and to \fBF\fP for blastpgp,
impala, and rpsblast.
.TP
\fB\-F\fP (seedtop)
Filter sequence with SEG.
.TP
\fB\-G\fP\ \fIN\fP (bl2seq)
Opening a gap costs \fIN\fP (-1 invokes default behavior; anything
else can result in unreliable statistics)
.TP
\fB\-G\fP\ \fIN\fP (blastall, blastcl3, megablast)
Opening a gap costs \fIN\fP (zero invokes default behavior)
.TP
\fB\-G\fP\ \fIN\fP (blastpgp, impala, seedtop)
Opening a gap costs \fIN\fP (default is 11)
.TP
\fB\-H\fP\ \fIN\fP (blastpgp)
End of required region in query (-1 indicates end of query)
.TP
\fB\-H\fP (impala)
Print help (different from usage message)
.TP
\fB\-H\fP\ \fIN\fP (megablast)
Maximal number of HSPs to save per database sequence (default is 0, unlimited)
.TP
\fB\-I\fP\ \fIstr\fP (bl2seq)
Location on first sequence
.TP
\fB\-I\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
Show GI's in deflines
.TP
\fB\-J\fP\ \fIstr\fP (bl2seq)
Location on second sequence
.TP
\fB\-J\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
Believe the query defline
.TP
\fB\-K\fP\ \fIN\fP (blastall, blastcl3, blastpgp)
Number of best hits from a region to keep (off by default, if used a
value of 100 is recommended)
.TP
\fB\-L\fP\ \fIstart,stop\fP (blastall, blastcl3, megablast, rpsblast)
Location on query sequence (for rpsblast, only valid in blastp mode)
.TP
\fB\-M\fP\ \fIstr\fP (bl2seq, blastall, blastcl3, blastpgp, impala, seedtop)
Use matrix \fIstr\fP (default = BLOSUM62)
.TP
\fB\-M\fP\ \fIN\fP (megablast)
Maximal total length of queries for a single search (default = 20000000)
.TP
\fB\-N\fP\ \fIX\fP (blastpgp, rpsblast)
Number of bits to trigger gapping (default = 22.0)
.TP
\fB\-N\fP\ \fIN\fP (megablast)
Type of a discontiguous word template:
.RS
.PD 0
.IP 0
coding (default)
.IP 1
optimal
.IP 2
two simultaneous
.PD
.RE
.TP
\fB\-O\fP\ \fIfilename\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
Write sequence alignments to \fIfilename\fP; only valid for
blastpgp, impala, rpsblast, and seedtop with \fB\-J\fP, and only valid
for megablast with \fB\-D2\fP.
.TP
\fB\-P\fP\ \fIN\fP (blastall, blastpgp, rpsblast)
Set to 1 for single-hit mode or 0 for multiple-hit mode (default)
.TP
\fB\-P\fP\ \fIfilename\fP (impala)
Read matrix profiles from database \fIfilename\fP
.TP
\fB\-P\fP\ \fIN\fP (megablast)
Maximal number of positions for a hash value (set to 0 [default] to ignore)
.TP
\fB\-Q\fP\ \fIN\fP (blastall, blastcl3)
Translate query according to genetic code \fIN\fP in
/usr/share/ncbi/data/gc.prt (default is 1)
.TP
\fB\-Q\fP\ \fIfilename\fP (blastpgp)
Output File for PSI-BLAST Matrix in ASCII
.TP
\fB\-Q\fP\ \fIfilename\fP (megablast)
Masked query output
.TP
\fB\-R\fP\ \fIfilename\fP (blastall)
Read PSI-TBLASTN checkpoint file \fIfilename\fP
.TP
\fB\-R\fP (blastcl3)
RPS Blast search
.TP
\fB\-R\fP\ \fIfilename\fP (blastpgp)
Input File for PSI-BLAST Restart
.TP
\fB\-R\fP (megablast)
Report the log information at the end of output
.TP
\fB\-S\fP\ \fIN\fP (bl2seq, blastall, blastcl3, megablast)
Query strands to search against database for blastn, blastx, tblastx:
.RS
.PD 0
.IP 1
top
.IP 2
bottom
.IP 3
both (default)
.PD
.RE
.TP
\fB\-S\fP\ \fIN\fP (blastpgp)
Start of required region in query (default = 1)
.TP
\fB\-S\fP\ \fIN\fP (seedtop)
Cutoff cost (default = 30)
.TP
\fB\-T\fP (bl2seq, blastall, blastcl3, blastpgp, megablast, rpsblast)
Produce HTML output
.TP
\fB\-U\fP (bl2seq, blastall, blastcl3, blastpgp, megablast, rpsblast)
Use lower case filtering for the query sequence
.TP
\fB\-W\fP\ \fIN\fP (bl2seq, blastall, blastcl3, blastpgp, megablast, rpsblast)
Use words of size \fIN\fP (length of best perfect match; zero invokes
default behavior, except with megablast, which defaults to 28, and
blastpgp, which defaults to 3.  The default values for the other
commands vary with "program": 11 for blastn, 28 for megablast, and 3
for everything else.)
.TP
\fB\-X\fP\ \fIN\fP (bl2seq, blastall, blastcl3, blastpgp, megablast, rpsblast, seedtop)
X dropoff value for gapped alignment (in bits) (zero invokes default
behavior, except with megablast, which defaults to 20, and rpsblast
and seedtop, which default to 15.  The default values for the other
commands vary with "program": 30 for blastn, 20 for megablast, 0 for
tblastx, and 15 for everything else.)
.TP
\fB\-Y\fP\ \fIX\fP (bl2seq, blastall, blastcl3, blastpgp, rpsblast)
Effective length of the search space (use zero for the real size)
.TP
\fB\-Z\fP\ \fIN\fP (blastall, blastcl3, blastpgp, megablast, rpsblast)
X dropoff value for final [dynamic programming?] gapped alignment in
bits (default is 50 for blastn and megablast, 0 for tblastx, 25 for
others)
.TP
\fB\-a\fP\ \fIfilename\fP (bl2seq)
Write SeqAnnot output to \fIfilename\fP
.TP
\fB\-a\fP\ \fIN\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast)
Number of processors to use (default is one)
.TP
\fB\-b\fP\ \fIN\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast, seedtop)
Number of database sequences to show alignments for (B) (default is 250)
.TP
\fB\-c\fP\ \fIN\fP (blastpgp, impala)
Constant in pseudocounts for multipass version (default is 9)
.TP
\fB\-d\fP\ \fIN\fP (bl2seq)
Use theoretical DB size of \fIN\fP (zero stands for the real size)
.TP
\fB\-d\fP\ \fIstr\fP (blastall, blastcl3, blastpgp, impala, megablast, seedtop)
Database to use (default is nr)
.TP
\fB\-d\fP\ \fIfilename\fP (rpsblast)
RPS BLAST Database
.TP
\fB\-e\fP\ \fIX\fP
Expectation value (E) (default = 1e6 for megablast, 10.0 for
everything else)
.TP
\fB\-f\fP\ \fIN\fP (blastall, blastcl3)
Threshold for extending hits, default if zero: 0 for blastn and
megablast, 11 for blastp, 12 for blastx, and 13 for tblasn and
tblastx.
.TP
\fB\-f\fP\ \fIN\fP (blastpgp)
Threshold for extending hits (default 11)
.TP
\fB\-f\fP (megablast)
Show full IDs in the output (default - only GIs or accessions)
.TP
\fB\-g\ F\fP (bl2seq, blastall, blastcl3, blastpgp, rpsblast)
Do not perform gapped alignment (N/A for tblastx)
.TP
\fB\-g\fP (megablast)
Generate words for every base of the database (default is every 4th)
.TP
\fB\-h\fP\ \fIX\fP (blastpgp, impala)
e-value threshold for inclusion in multipass model (default = 0.005)
.TP
\fB\-i\fP\ \fIfilename\fP
Read (first) sequence from \fIfilename\fP (default is stdin)
.TP
\fB\-j\fP\ \fIfilename\fP (bl2seq)
Read second sequence from \fIfilename\fP
.TP
\fB\-j\fP\ \fIN\fP (blastpgp)
Maximum number of passes to use in multipass version (default = 1)
.TP
\fB\-k\fP\ \fIfilename\fP (blastpgp, seedtop)
Input hit file for PHI-BLAST (default = hit_file)
.TP
\fB\-l\fP\ \fIstr\fP (blastall, blastpgp, megablast)
Restrict search of database to list of GI's [String]
.TP
\fB\-l\fP\ \fIfilename\fP (rpsblast)
Logfile name (default is rpsblast.log)
.TP
\fB\-m\fP (bl2seq)
Use Mega Blast for search
.TP
\fB\-m\fP\ \fIN\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast)
alignment view options:
.RS
.PD 0
.IP 0
pairwise (default)
.IP 1
query-anchored showing identities
.IP 2
query-anchored, no identities
.IP 3
flat query-anchored, show identities
.IP 4
flat query-anchored, no identities
.IP 5
query-anchored, no identities and blunt ends
.IP 6
flat query-anchored, no identities and blunt ends
.IP 7
XML Blast output (not available for impala)
.IP 8
tabular (not available for impala)
.IP 9
tabular with comment lines (not available for impala)
.IP 10
ASN.1 text (not available for impala or rpsblast)
.IP 11
ASN.1 binary (not available for impala or rpsblast)
.PD
.RE
.TP
\fB\-n\fP (blastall, blastcl3)
MegaBlast search
.TP
\fB\-n\fP (megablast)
Use non-greedy (dynamic programming) extension for affine gap scores
.TP
\fB\-o\fP\ \fIfilename\fP
Write report (alignment output) to \fIfilename\fP rather than stdout
.TP
\fB\-p\fP\ \fIstr\fP (bl2seq, blastall, blastcl3)
Use the "program" (comparison type) \fIstr\fP.  The \fBDESCRIPTION\fP
section covers this option in more detail.
.TP
\fB\-p\fP\ \fIstr\fP (blastpgp)
program option for PHI-BLAST (default = blastpgp)
.TP
\fB\-p\fP\ \fIX\fP (megablast)
Identity percentage cut-off (default = 0)
.TP
\fB\-p\ F\fP (rpsblast)
Query sequence is nucleotide, not protein
.TP
\fB\-p\fP\ \fIstr\fP (seedtop)
program name:
.RS
.PD 0
.IP patmatchp 10
indicates which patterns occur in a sequence
.IP patternp 10
indicates which sequences contain a pattern
.PD
.RE
.TP
\fB\-q\fP\ \fIN\fP (bl2seq, blastall, blastcl3, megablast, seedtop)
Penalty for a nucleotide mismatch (blastn only) (default = -10 for
seedtop, -3 for everything else)
.TP
\fB\-r\fP\ \fIN\fP (bl2seq, blastall, blastcl3, megablast, seedtop)
Reward for a nucleotide match (blastn only) (default = 10 for seedtop,
-10 for everything else)
.TP
\fB\-s\fP (blastpgp)
Compute locally optimal Smith-Waterman alignments
.TP
\fB\-s\fP\ \fIN\fP (megablast)
Minimal hit score to report (0 for default behavior)
.TP
\fB\-t\fP\ \fIN\fP (bl2seq, blastall, blastcl3)
Length of the largest intron allowed in tblastn for linking HSPs (default = 0)
.TP
\fB\-t\ F\fP (blastpgp)
Do not use composition-based statistics
.TP
\fB\-t\fP\ \fIN\fP (megablast)
Length of a discontiguous word template (contiguous word if 0 [default])
.TP
\fB\-u\fP\ \fIstr\fP (blastcl3)
Restrict search of database to results of Entrez2 lookup
.TP
\fB\-v\fP\ \fIN\fP (blastall, blastcl3, blastpgp, impala, megablast,
rpsblast, seedtop)
Number of one-line descriptions to show (V) (default = 500)
.TP
\fB\-w\fP\ \fIN\fP (blastall, blastcl3)
Frame shift penalty (OOF algorithm for blastx)
.TP
\fB\-y\fP\ \fIX\fP (blastall, blastcl3, blastpgp, impala, rpsblast)
X dropoff for ungapped extensions in bits (0.0 invokes default
behavior: 20 for blastn, 10 for megablast, and 7 for all others.)
.TP
\fB\-y\fP\ \fIN\fP (megablast)
X dropoff value for ungapped extension (default is 10)
.TP
\fB\-z\fP\ \fIN\fP (blastall, blastcl3, blastpgp, impala, megablast, rpsblast)
Effective length of the database (use zero for the real size)
.SH BUGS
This manual page is long and confusing; individual pages might be better.
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.ad l
.BR blastclust (1),
.BR copymat (1),
.BR fastacmd (1),
.BR formatdb (1),
.BR makemat (1),
blast.txt,
<http://www.ncbi.nlm.nih.gov/BLAST/>