method: srsis really a special case of
method: externalwith some additional features.
SRS is a powerful database querying system that can cross reference between different databases, launch applications and so on. SRS can be run either through a web interface (see the description of the URL method above for an example) or via the command line program getz. Indexing and configuring databases for SRS is outside the scope of this document which will describe how to connect to preconfigured and indexed SRS databases.3.9 If getz is already in your
PATHenvironment variable then insert the following (or similar) in your
DB emblgetz [ type: N method: srs release: "63" format: embl comment: 'EMBL using getz' dbalias: embl app: getz ]
This will provide access to the SRS database 'embl' as
emblgetz:acc. If the SRS database has a different name to the EMBOSS database (as is the case here) then the
dbalias:tag should be used to access the correct SRS database.
This configuration can be extremely slow for the all access mode. It is probably a better idea to set up the database as follows:
DB emblgetz [ type: N methodquery: srs release: "63" format: embl comment: 'EMBL using getz' dbalias: embl app: getz methodall: direct file: "*.dat" dir: \$emboss_db_dir/embl ]
which will use
method: srsfor the
queryaccess mode but will use
method: directfor the
allaccess mode, thus speeding up reading of the whole database.
The SRSFASTA access method is identical to the normal SRS method except that it returns the sequence in FASTA format and so does not need a