HMMER User's Guide

| Dept. of Genetics | WashU | Medical School | Sequencing Center | CGM | IBC| | Eddy lab | Internal (lab only) | HMMER | PFAM | tRNAscan-SE | Software | Publications |

getseq - get a sequence from a flatfile database.

Synopsis

getseq [options] seqname

Description

getseq 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 GSI 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). GSI indexing is recommended for all large or permanent databases.

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.