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:

-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):

-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:

-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¶

AUTHOR¶

The National Center for Biotechnology Information.

SEE ALSO¶

blast(1), /usr/share/doc/blast2/fastacmd.html.