[Bioperl-l] Uniprot/Swiss accessions?

[Cook, Malcolm]

you could:

1) Use eutils search with -database protein -term "srcdb swiss prot"[Properties]
  If you use a retmax of 100000 it should only take a few seconds to download the 458,445 ginumbers.
  I just did it.

2) use fastacmd to extract the fasta from nr for these gis, and parse the defline.
  (assuming you have a copy of nr)


Does this work for you?


Malcolm Cook
Stowers Institute for Medical Research - Kansas City, Missouri
  

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org 
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of 
> Smithies, Russell
> Sent: Sunday, May 17, 2009 11:53 PM
> To: 'BioPerl List'
> Subject: [Bioperl-l] Uniprot/Swiss accessions?
> 
> Does anyone know of a way to get GI numbers for 
> Uniprot/Swissprot accessions?
> 
> Fasta from Uniprot's FTP site doesn't formatdb correctly 
> (with the -o T option) as it's missing the gi number in the 
> fasta header.
> NCBI won't let you use SwissProt ids in batch-entrez and I 
> don't want to have to look up all 466,739 of them.
> I could use Bio::DB::Eutilities and query each id but even at 
> 10 queries/second (the limit changed recently) it would take too long.
> 
> Any ideas?
> Is there a swissprot2gi list somewhere?
> 
> Thanx,
> 
> 
> Russell Smithies 
> 
> Bioinformatics Applications Developer
> T +64 3 489 9085
> E  russell.smithies at agresearch.co.nz 
> 
> Invermay  Research Centre
> Puddle Alley,
> Mosgiel,
> New Zealand
> T  +64 3 489 3809
> F  +64 3 489 9174
> www.agresearch.co.nz 
> 
> 
> 
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