[Bioperl-l] Uniprot/Swiss accessions?

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon May 18 04:53:05 UTC 2009

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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