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fastacmd(1) [debian man page]

FASTACMD(1)						     NCBI Tools User's Manual						       FASTACMD(1)

fastacmd - retrieve FASTA sequences from a BLAST database SYNOPSIS
fastacmd [-] [-D N] [-I] [-L start,stop] [-P N] [-S N] [-T] [-a] [-c] [-d str] [-i str] [-l N] [-o filename] [-p type] [-s str] [-t] DESCRIPTION
fastacmd retrieves FASTA formatted sequences from a blast(1) database formatted using the `-o' option. An example fastacmd call would be fastacmd -d nr -s p38398 OPTIONS
A summary of options is included below. - Print usage message -D N Dump the entire database in some format: 1 fasta 2 GI list 3 Accession.version list -I Print database information only (overrides all other options) -L start,stop Range of sequence to extract (0 in start is beginning of sequence, 0 in stop is end of sequence, default is whole sequence) -P N Retrieve sequences with Protein Identification Group (PIG) N. -S N Strand on subsequence (nucleotide only): 1 top (default) 2 bottom -T Print taxonomic information for requested sequence(s) -a Retrieve duplicate accessions -c Use ^A (01) as non-redundant defline separator -d str Database (default is nr) -i str Input file with GIs/accessions/loci for batch retrieval -l N Line length for sequence (default = 80) -o filename Output file (default = stdout) -p type Type of file: G guess (default): look for protein, then nucleotide T protein F nucleotide -s str Comma-delimited search string(s). GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag' -t Definition line should contain target GI only EXIT STATUS
0 Completed successfully. 1 An error (other than those below) occurred. 2 The BLAST database was not found. 3 A search (accession, GI, or taxonomy info) failed. 4 No taxonomy database was found. AUTHOR
The National Center for Biotechnology Information. SEE ALSO
blast(1), /usr/share/doc/blast2/fastacmd.html. NCBI
2005-11-04 FASTACMD(1)

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FORMATRPSDB(1)						     NCBI Tools User's Manual						    FORMATRPSDB(1)

formatrpsdb - Build databases for RPS Blast SYNOPSIS
formatrpsdb [-] [-E N] [-G N] [-S X] [-U str] [-b] [-f X] -i filename [-l filename] [-n str] [-o] [-t str] [-v N] DESCRIPTION
Formatrpsdb is a utility that converts a collection of input sequences into a database suitable for use with Reverse Position Specific (RPS) Blast. Each input sequence, together with its position-specific scoring matrix (PSSM), is ASN.1 encoded into a PssmWithParameters (or `scoremat') object and resides in a separate file. Scoremat objects can be created using blastpgp. Formatrpsdb is given a list of these files and produces the corresponding database. Formatrpsdb is designed to perform the work of formatdb, makemat and copymat simultaneously, without generating the large number of inter- mediate files these utilities would need to create an RPS Blast database. Further, scoremat objects are in more general use than the binary format makemat requires. It is hoped that direct manipulation of scoremat objects will encourage conversion of more diverse sequence collections into RPS Blast databases. Databases generated by formatrpsdb are binary compatible with databases generated by formatdb/makemat/copymat, although the database files will in general not be byte- for-byte identical. OPTIONS
A summary of options is included below. - Print usage message -E N The gap extension penalty (if not specified in the scoremat; default = 1) -G N The gap opening penalty (if not specified in the scoremat; default = 11) -S X For scoremats that contain only residue frequencies, the scaling factor to apply when creating PSSMs (default = 100) -U str Underlying score matrix (if not specified in the scoremat; default = BLOSUM62) -b Scoremat files are binary (vs. text) ASN1. -f X Threshold for extending hits for RPS database (default = 11) -i filename Input file containing list of ASN.1 Scoremat filenames -l filename Log file name (default = formatrpsdb.log) -n str Base name of output database (same as input file if not specified) -o Create index files for database -t str Title for database file -v N Database volume size in millions of letters (default = 0, which really means no limit) AUTHOR
The National Center for Biotechnology Information. SEE ALSO
blast(1), copymat(1), formatdb(1), makemat(1), /usr/share/doc/blast2/formatrpsdb.html NCBI
2004-10-20 FORMATRPSDB(1)

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