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fastacmd - retrieve FASTA sequences from a BLAST database


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]


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


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


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.

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