[EMBOSS] EMBOSS database setup
Hamish McWilliam
hpm at bioinfo-user.org.uk
Sun Dec 3 15:06:25 UTC 2006
Hi Alan,
> The appended definitions are simple ones that may be
> useful if you only want a few sequences at a time.
> If sites upgrade to SRS8 then alter accordingly.
>
> Alan
>
> DB embl [ type: N method: srswww format: embl release: "EBI"
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> comment: "EMBL from the EBI" ]
>
> DB em [ type: N method: srswww format: embl release: "EBI"
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> dbalias: "EMBL"
> comment: "EMBL from the EBI" ]
>
> DB swissprot [ type: P method: srswww format: swiss release: "EBI"
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> comment: "SWISSPROT from the EBI" ]
>
> DB sw [ type: P method: srswww format: swiss release: "EBI"
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> dbalias: "SWISSPROT"
> comment: "SWISSPROT from the EBI" ]
>
> DB uniprot [ type: P method: srswww format: swiss release: "EBI"
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> comment: "UNIPROT from the EBI" ]
>
> DB uni [ type: P method: srswww format: swiss release: EBI
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> dbalias: "UNIPROT"
> comment: "UNIPROT from the EBI" ]
>
> DB pir [ type: P method: srswww format: nbrf release: "EBI"
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> comment: "PIR from the EBI" ]
>
> DB genbank [ type: N method: srswww format: genbank release: "NCBI"
> url: "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz"
> comment: "GenBank from Infobiogen" ]
>
> DB gb [ type: N method: srswww format: genbank release: "NCBI"
> url: "http://www.infobiogen.fr/srs7bin/cgi-bin/wgetz"
> dbalias: "GENBANK"
> comment: "GenBank from Infobiogen" ]
>
> DB refseq [ type: N method: srswww format: genbank release: "NCBI"
> url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
> comment: "REFSEQ from EBI" ]
For the EBI's SRS server please use:
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz
as the URL. This should allow for continued support when the server is
upgraded.
Also note that the Infobiogen SRS service is no longer available. For
other SRS sites carrying GenBank please see the Public SRS Server List
(http://downloads.biowisdomsrs.com/publicsrs.html).
Hamish
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