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sfetch

NAME

sfetch - get a sequence from a flatfile database.

SYNOPSIS

sfetch [options] seqname

DESCRIPTION

sfetch retrieves the sequence named seqname from a sequence database.

Which database is used is controlled by the -d and -D options, or "little databases" and "big databases". The directory location of "big databases" can be specified by environment variables, such as $SWDIR for Swissprot, and $GBDIR for Genbank (see -D for complete list). A complete file path must be specified for "little databases". By default, if neither option is specified and the name looks like a Swissprot identifier (e.g. it has a _ character), the $SWDIR environment variable is used to attempt to retrieve the sequence seqname from Swissprot.

A variety of other options are available which allow retrieval of subsequences (-f,-t); retrieval by accession number instead of by name (-a); reformatting the extracted sequence into a variety of other formats (-F); etc.

If the database has been SSI indexed, sequence retrieval will be extremely efficient; else, retrieval may be painfully slow (the entire database may have to be read into memory to find seqname). SSI indexing is recommended for all large or permanent databases. The program sindex creates SSI indexes for any sequence file.

sfetch was originally named getseq, and was renamed because it clashed with a GCG program of the same name.

OPTIONS

-a

Interpret seqname as an accession number, not an identifier.

-d <seqfile>

Retrieve the sequence from a sequence file named <seqfile>. If a GSI index <seqfile>.gsi exists, it is used to speed up the retrieval.

-f <from>

Extract a subsequence starting from position <from>, rather than from 1. See -t. If <from> is greater than <to> (as specified by the -t option), then the sequence is extracted as its reverse complement (it is assumed to be nucleic acid sequence).

-h

Print brief help; includes version number and summary of all options, including expert options.

-o <outfile>

Direct the output to a file named <outfile>. By default, output would go to stdout.

-r <newname>

Rename the sequence <newname> in the output after extraction. By default, the original sequence identifier would be retained. Useful, for instance, if retrieving a sequence fragment; the coordinates of the fragment might be added to the name (this is what Pfam does).

-t <to>

Extract a subsequence that ends at position <to>, rather than at the end of the sequence. See -f. If <to> is less than <from> (as specified by the -f option), then the sequence is extracted as its reverse complement (it is assumed to be nucleic acid sequence)

-D <database>

Retrieve the sequence from the main sequence database coded <database>. For each code, there is an environment variable that specifies the directory path to that database. Recognized codes and their corresponding environment variables are -Dsw (Swissprot, $SWDIR); -Dpir (PIR, $PIRDIR); -Dem (EMBL, $EMBLDIR); -Dgb (Genbank, $GBDIR); -Dwp (Wormpep, $WORMDIR); and -Dowl (OWL, $OWLDIR). Each database is read in its native flatfile format.

-F <format>

Reformat the extracted sequence into a different format. (By default, the sequence is extracted from the database in the same format as the database.) Available formats are embl, fasta, genbank, gcg, strider, zuker, ig, pir, squid, and raw.

EXPERT OPTIONS

--informat <s>

Specify that the sequence file is in format <s>, rather than the default FASTA format. Common examples include Genbank, EMBL, GCG, PIR, Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete list of accepted format names. This option overrides the default format (FASTA) and the -B Babelfish autodetection option.

SEE ALSO

afetch(1), alistat(1), compalign(1), compstruct(1), revcomp(1), seqsplit(1), seqstat(1), shuffle(1), sindex(1), sreformat(1), stranslate(1), weight(1).

AUTHOR

Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) See COPYING in the source code distribution for more details, or contact me.

 Sean Eddy
 HHMI/Department of Genetics
 Washington University School of Medicine
 4444 Forest Park Blvd., Box 8510
 St Louis, MO 63108 USA
 Phone: 1-314-362-7666
 FAX  : 1-314-362-2157
 Email: eddy@genetics.wustl.edu