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Man Pages


Manual Reference Pages  -  FASTACMD (1)

NAME

fastacmd - retrieve FASTA sequences from a BLAST database

CONTENTS

Synopsis
Description
Options
Exit Status
Author
See Also

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, \(aqgnl|dbname|tag\(aq
-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), fastacmd.html.
Search for    or go to Top of page |  Section 1 |  Main Index


NCBI FASTACMD (1) 2005-11-04

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