--- name: "sfetch" section: "1" platform: "linux" package: "biosquid" version: "1.9g+cvs20050121-15.1+b2" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/sfetch" --- # sfetch(1) ## 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** *\* Retrieve the sequence from a sequence file named *\.* If a GSI index *\.gsi* exists, it is used to speed up the retrieval. - **-f** *\* Extract a subsequence starting from position *\,* rather than from 1. See **-t.** If *\* is greater than *\* (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** *\* Direct the output to a file named *\.* By default, output would go to stdout. - **-r** *\* Rename the sequence *\* 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** *\* Extract a subsequence that ends at position *\,* rather than at the end of the sequence. See **-f.** If *\* is less than *\* (as specified by the **-f** option), then the sequence is extracted as its reverse complement (it is assumed to be nucleic acid sequence) - **-D** *\* Retrieve the sequence from the main sequence database coded *\. 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** *\* 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** *\* Specify that the sequence file is in format *\,* 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)](/afetch/1.md), [**alistat**(1)](/alistat/1.md), [**compalign**(1)](/compalign/1.md), [**compstruct**(1)](/compstruct/1.md), [**revcomp**(1)](/revcomp/1.md), [**seqsplit**(1)](/seqsplit/1.md), [**seqstat**(1)](/seqstat/1.md), [**shuffle**(1)](/shuffle/1.md), [**sindex**(1)](/sindex/1.md), [**sreformat**(1)](/sreformat/1.md), [**stranslate**(1)](/stranslate/1.md), [**weight**(1)](/weight/1.md). ## 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 ```