FASTACMD(1)
NAME
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 (\001) 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.