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.