IMPALA: Integrating Matrix Profiles And Local Alignments 1. Files in Distribution The following IMPALA source code files are distributed: copymat.c impatool.c makemat.c posit2.c profiles.c newkar.c profiles.h Makefile 2. Compilation Run the following commands in the directory, containing IMPALA source code files: make makemat make copymat make impala This will result in three binary executable files: 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); impala : search program (searches a database of score matrices, prepared by copymat, producing BLAST-like output). 3. Conversion of profiles into searchable database 3.1. 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 .pn; iv. a list of master sequence file names, one per line, in the same order as a list of profile names, named .sn; The following files will be created: i. a collection of ASCII files, corresponding to each of the original profiles, named .mtx; ii. a list of ASCII matrix files, named .mn; iii. ASCII file with auxiliary information, named .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 impala. 3.1. Secondary preprocessing Prepare the following files: i. a collection of ASCII files, corresponding to each of the original profiles, named .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 .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 .sn; v. ASCII file with auxiliary information, named .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: i. a huge binary file, containing all profile matrices, named .mat; Arguments to copymat -P database name (required) -H get help (overrides all other arguments) 4. Search Before you start searching, check that you have copies of or soft links to all the files associated with the PSSM library. If the library has K PSSMs, you should have K files with names ending in .mtx K files with names ending in a 3-letter extension starting with c 1 file with name ending in .pn 1 file with name ending in .sn 1 file with name ending in .aux 1 file with name ending in .mn 1 file with name ending in .mat Arguments to impala -i query sequence file (required) -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 -H get help (overrides all other options) 5. Directory convention Since IMPALA requires a large number of files, it may be convenient to store your impala files in various directories. For copymat, makemat, and impala the following parsing convention applies to the string that follows the -P argument. If the string starts with a '/', then it is deemed to be a full path name. Whatever prefix occurs upto and including the rightmost '/' is deemed to be a prefix that should be prepended to all file names in the .sn, .pn, and .mn files. Example: If you call any of the 3 programs including the argument -P /foo/bar/wolf1187 then /foo/bar/ is prepended to every filename listed in wolf1187.pn wolf1187.sn wolf1187.mn before opening the file, but the files wolf1187.pn wolf1187.sn wolf1187.mn themselves are not changed. 6. Output IMPALA output closely mimics output of BLASTP family programs and should be compatible with SEALS BLAST parsers. Send suggestions, comments, complaints only to Alejandro Schaffer schaffer@helix.nih.gov Reference: Schaffer, A.A., Wolf, Y.I., Ponting, C.P. Koonin, E.V., Aravind, L., Altschul, S. F., IMPALA: Matching a Protein Sequence Against a Collection of PSI-BLAST-Constructed Position-Specific Score Matrices, Bioninformatics, to appear. Please cite the above paper if you publish any results computed by IMPALA.