[WashU] 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 |

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Subsections

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


next up previous contents
Next: seqstat - show statistics Up: Manual pages Previous: alistat - show statistics


Direct comments and questions to <eddy@genetics.wustl.edu>