Need suggestions for sequence retrieval

Peter Rice pmr at sanger.ac.uk
Tue Dec 19 09:16:36 EST 1995


In article <Andy.Law-1912951113020001 at pc0734.ri.bbsrc.ac.uk> Andy.Law at bbsrc.ac.uk (Andy Law) writes:
>   I would like to add the capability for downloading the sequence of
>   interest directly to the desktop. Has anyone got any suggestions as to how
>   to do that. I thought about driving Netscape to pull the sequence from an
>   SRS server, but the syntax of the URL will obviously differ from location
>   to location. Is there a standard way that I can do this, or will I have to
>   put a dirty hack in to cover as many options as possible.

You can guarantee that all SRSWWW sites will use a URL of the form

http://www.site.address:port/srs/srsc?[EMBL-id:XXXXXX]+-sf+EMBL

(You can also use -sf+PIR, -sf+FASTA and -sf+GCG but beware of GCG
as some sites keep the ".." in the feature tbale, while others have gapped it)

The "/srs/srsc" is fixed in SRS 4. Otherwise the status page query does not
work from other sites.

All you need is a list of sites (and port numbers) with EMBL, which
you can get from the SRS status pages (for example our status page, at
http://www.sanger.ac.uk/srs/status.html). The port numbers (default is
80) show up on the site links. Go down to "EMBL" and you will see all
sites with the EMBL database available.

You can do the same for GENBANK, SWISSPROT and any other databases you need.
Users can then pick the site nearest them, and you can set a default to a
site that gives a fast response for most users.

You may need a few extra tricks if your BLAST searches cover EMNEW and
SWISSNEW as well, and you can hit the dreaded "what's the accession
number problem" if BLAST returns an entry name, and the SRS site has a
more recent entry name.
--
------------------------------------------------------------------------
Peter Rice                           | Informatics Division
E-mail: pmr at sanger.ac.uk             | The Sanger Centre
Tel: (44) 1223 494967                | Hinxton Hall, Hinxton,
Fax: (44) 1223 494919                | Cambs, CB10 1RQ
URL: http://www.sanger.ac.uk/~pmr/   | England




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