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fastacmd

Langue: en

Autres versions - même langue

Version: 256396 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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.
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hommes.
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