[Bioperl-l] Uniprot/Swiss accessions?
MEC at stowers.org
Mon May 18 10:34:39 EDT 2009
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?
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?
> Russell Smithies
> Bioinformatics Applications Developer
> T +64 3 489 9085
> E russell.smithies at agresearch.co.nz
> Invermay Research Centre
> Puddle Alley,
> New Zealand
> T +64 3 489 3809
> F +64 3 489 9174
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