[BiO BB] RefSeq Accession Numbers

[Hamid Nikbakht]

Dear Peter,
It seems it works but I should check it along my accession numbers.
Thak you for your care,
Yours,
Hamid

/*
Hamid( Behnam )Nikbakht,
M.Sc of Cell and Molecular Sciences
Bioinformatics Center
Laboratory of Biophysics and Molecular Biology
Institute of Biochemistry and Biophysics
University of Tehran
P.O.Box 13145-1384
Tehran, Iran.
Tel: (+98 21) 664-98672
Fax: (+98 21) 669-56985
Alt. E-Mail : hamid at ibb.ut.ac.ir
*/


-----Original Message-----
From: pmr at ebi.ac.uk
To: "The general forum at Bioinformatics.Org" 
<bio_bulletin_board at bioinformatics.org>
Cc: ebisrs at ebi.ac.uk
Date: Fri, 16 Jun 2006 21:55:53 +0100 (BST)
Subject: Re: [BiO BB] RefSeq Accession Numbers

> Hi Hamid,
> 
> > I tried this :
> >
> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]>un
> iprot+-ascii
> > but this error has been shown:
> > Error:No Entries found
> > when I remove the last part (>uniprot)
> >
> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]+-a
> scii
> > it retrieves the result for AP_000714.
> > but for your accession number:uniprot-acc:P13569 the reverse
> retrieves
> > NP_000483 and when I try:
> >
> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000483]>un
> iprot+-ascii
> > I get the result ... It is strange!
> 
> Interesting ... it depends on how the links are built. One weakness in
> SRS
> is that there is only one default path for links, but you can also make
> them explicit.
> 
> I may have been wrong in assuming links will go through UniParc. We had
> an
> example last year where we found links - not at EBI but at another SRS
> server - between Genbank and RefSeq defaulted to going through the
> taxonomy database (start with one human gene, find them all!!!)
> 
> I suspect in this case the route is not through UniParc. It could be
> entrezgene or IPI, both of which fail for your entry. We can check and
> maybe find a better preferred link that will include bacterial
> proteins.
> 
> You can force the route through UniParc with an extra redirect:
> 
> http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[refseqp-acc:AP_000714]>un
> iparc>uniprot+-ascii
> 
> (If email mangles that, I added ">uniparc" before ">uniprot" in your
> refseq to uniprot link).
> 
> You can also just link to UniParc and choose your own links.
> 
> Hope that helps,
> 
> Peter Rice
> 
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