Configuring EMBOSS to use SRS for database lookup.

method: srs

is really a special case of

method:
external

with 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

PATH

environment variable then insert the following (or similar) in your

.embossrc

:

 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: srs

for the

query

access mode but will use

method: direct

for the

all

access 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

format:

tag.