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.
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− |
Print usage message |
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−D N |
Dump the entire database in some format: |
1
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fasta |
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2 |
GI list |
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3 |
Accession.version list |
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−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)
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−P N |
Retrieve sequences with Protein Identification Group (PIG) N. | ||
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−S N |
Strand on subsequence (nucleotide only): |
1
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top (default) |
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2 |
bottom |
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−T |
Print taxonomic information for requested sequence(s)
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−a |
Retrieve duplicate accessions | ||
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−c |
Use ^A (\001) as non-redundant defline separator | ||
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−d str |
Database (default is nr) | ||
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−i str |
Input file with GIs/accessions/loci for batch retrieval | ||
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−l N |
Line length for sequence (default = 80) |
−o filename
Output file (default = stdout)
−p type
Type of file:
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G |
guess (default): look for protein, then nucleotide | ||
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T |
protein | ||
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F |
nucleotide | ||
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−s str |
Comma-delimited search string(s). GIs, accessions, loci, or fullSeq-id strings may be used, e.g., 555, AC147927, 'gnl|dbname|tag'
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−t |
Definition line should contain target GI only |
EXIT STATUS
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0 |
Completed successfully. | ||
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1 |
An error (other than those below) occurred. | ||
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2 |
The BLAST database was not found. | ||
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3 |
A search (accession, GI, or taxonomy info) failed. | ||
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4 |
No taxonomy database was found. |
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO
blast(1), /usr/share/doc/blast2/fastacmd.html.