problem with seqret and protein sequences.

[Peter Rice]

"michael hanlon (BITS)" wrote:
> 
> Due to changes in format at Sanger, we have edited our emboss.default to use the SRS service at EBI instead. Heres the relevant part:
> 
> DB swall [ type: P method: url format: embl
>   url: "http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWall-id:%s]"
>   comment: "EBI Swissprot IDs and Trembl IDs" ]
>
> DB embl [ type: N method: url format: embl
>   url: "http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[EMBLRELEASE-ID:%s]"
>   comment: EBI EMBL ACs" ]
>
> The embl bits work OK, but not the swall, I just get 'unable to read sequences'

You are lucky with EMBL :-) For SwissProt, you should add +-ascii to get
the URL to work. It depends on the default views defined for the EBI's SRS
server.

But, with EMBOSS 2.5.0 (should be fine with 2.4.1 too, though there was a
problem with chunked HTTP output) you can use method: srswww and define the
SRS database name in dbalias. With this definition you can use
swall-id:amir_pseae and swall-acc:P10932.

If you add fields: "sv des key org" you can search those too in the USA,
though beware of huge result sets because EMBOSS will keep them in memory.
A small search would be embl-org:aardvark (27 entries, at least until an
aardvark EST project starts :-) Without the fields definition you are safer
because users are less likely to generate a huge request to an SRS server
with an ID or ACC query.

Method: srswww builds the full SRS URL for you (with +-e+-ascii), and
converts the USA queries into SRS queries. It was added in EMBOSS 2.4.0.

For example:

DB swall [ type: P method: srswww format: embl
  url: "http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz"
  comment: "EBI Swissprot and Trembl" ]

DB embl [ type: N method: srswww format: embl
  url: "http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz"
  dbalias: emblrelease
  comment: EBI EMBL" ]

regards,

Peter Rice

-- 
------------------------------------------------
Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723