fastacmd(1)
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.
