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

[Stefanie Lager]

Using method: URL

you can also retrive entries from Swissprot (or UniProt) from
http://www.ebi.uniprot.org or via dbfetch
http://www.ebi.ac.uk/cgi-bin/dbfetch

Stefanie

> 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
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