[EMBOSS] EMBOSS database configurartion......

[Peter Rice]

Richard Rothery wrote:

> How does one configuire EMBOSS to retrieve sequences directly from
> swissprot/trembl? Specifically what lines have to be added to the
> database configuration file? Something that links to the EXPASY site?
> The idea here is to use SEQRET to grab the sequences. I have no room on
> my system for the entire database, indexing etc...

Using the EBI SRS server ... depends on which database you would like:

DB uniprot [
type: P
format: swiss
method: srswww
dbalias: uniprot
url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
]

DB sptrembl [
type: P
format: swiss
method: srswww
dbalias: sptrembl
url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
]

DB swissprot [
   type: P
   format: swiss
   method: srswww
   dbalias: swissprot
   url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz"
]

Using EXPASY's SRS server (in the USA):

Note the spelling of the database alias with an underscore

DB expasy [
   type: P
   format: swiss
   method: srswww
   dbalias: swiss_prot
   url: "http://us.expasy.org/srs5bin/cgi-bin/wgetz"
]

These will all search by ID and accession number


> Hopefully, the answer to this one will be simple!!

There will be many possible answers. These were just a few suggestions!


regards,

Peter Rice