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.TH FASTACMD 1 2005-11-04 NCBI "NCBI Tools User's Manual"
.SH NAME
fastacmd \- retrieve FASTA sequences from a BLAST database
.SH SYNOPSIS
.B fastacmd
[\|\fB\-\fP\|]
[\|\fB\-D\fP\ \fIN\fP\fP\|]
[\|\fB\-I\fP\|]
[\|\fB\-L\fP\ \fIstart\fP,\fIstop\fP\|]
[\|\fB\-P\fP\ \fIN\fP\|]
[\|\fB\-S\fP\ \fIN\fP\|]
[\|\fB\-T\fP\|]
[\|\fB\-a\fP\|]
[\|\fB\-c\fP\|]
[\|\fB\-d\fP\ \fIstr\fP\|]
[\|\fB\-i\fP\ \fIstr\fP\|]
[\|\fB\-l\fP\ \fIN\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fItype\fP\|]
[\|\fB\-s\fP\ \fIstr\fP\|]
[\|\fB\-t\fP\|]
.SH DESCRIPTION
\fBfastacmd\fP retrieves FASTA formatted sequences from a
\fBblast\fP(1) database formatted using the `\fB\-o\fP' option. An
example \fBfastacmd\fP call would be
.PP
.ce
fastacmd \-d nr \-s p38398
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-D\fP\ \fIN\fP
Dump the entire database in some format:
.RS
.PD 0
.IP 1
fasta
.IP 2
GI list
.IP 3
Accession.version list
.PD
.RE
.TP
\fB\-I\fP
Print database information only (overrides all other options)
.TP
\fB\-L\fP\ \fIstart\fP,\fIstop\fP
Range of sequence to extract (0 in start is beginning of sequence, 0
in stop is end of sequence, default is whole sequence)
.TP
\fB\-P\fP\ \fIN\fP
Retrieve sequences with Protein Identification Group (PIG) \fIN\fP.
.TP
\fB\-S\fP\ \fIN\fP
Strand on subsequence (nucleotide only):
.RS
.PD 0
.IP 1
top (default)
.IP 2
bottom
.PD
.RE
.TP
\fB\-T\fP
Print taxonomic information for requested sequence(s)
.TP
\fB\-a\fP
Retrieve duplicate accessions
.TP
\fB\-c\fP
Use ^A (\e001) as non-redundant defline separator
.TP
\fB\-d\fP\ \fIstr\fP
Database (default is nr)
.TP
\fB\-i\fP\ \fIstr\fP
Input file with GIs/accessions/loci for batch retrieval
.TP
\fB\-l\fP\ \fIN\fP
Line length for sequence (default = 80)
.TP
\fB\-o\fP\ \fIfilename\fP
Output file (default = stdout)
.TP
\fB\-p\fP\ \fItype\fP
Type of file:
.RS
.PD 0
.IP G
guess (default): look for protein, then nucleotide
.IP T
protein
.IP F
nucleotide
.PD
.RE
.TP
\fB\-s\fP\ \fIstr\fP
Comma-delimited search string(s).
GIs, accessions, loci, or fullSeq-id strings may be used,
\fIe.g.\fP, \fB555\fP, \fBAC147927\fP, \fB\(aqgnl|dbname|tag\(aq\fP
.TP
\fB\-t\fP
Definition line should contain target GI only
.SH EXIT STATUS
.RS
.PD 0
.IP 0
Completed successfully.
.IP 1
An error (other than those below) occurred.
.IP 2
The BLAST database was not found.
.IP 3
A search (accession, GI, or taxonomy info) failed.
.IP 4
No taxonomy database was found.
.PD
.RE
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR blast (1),
fastacmd.html.
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