[Bioperl-l] Uniprot/Swiss accessions?

[Chris Fields]

If you need to retain mapping between acc => gi it gets a little more  
complicated; most procedures to NCBI return a 'bag' of gi's w/o any  
relation to their original accession.  You can grab them via esummary,  
though, but you'll have to iterate through them.

The other option is LiveLists (has both nuc and protein acc => gi).   
I'm assuming this would have the swissprot accessions included (famous  
last words):

ftp://ftp.ncbi.nih.gov/genbank/livelists/README.genbank.livelists

chris



On May 18, 2009, at 9:34 AM, Cook, Malcolm wrote:

> 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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