[Bioperl-l] Uniprot/Swiss accessions?
Russell.Smithies at agresearch.co.nz
Mon May 18 19:11:40 EDT 2009
As far as I can see, none of the fasta at ftp://ftp.uniprot.org/pub/databases/uniprot_datafiles_by_format/fasta/ will correctly formatdb with the "-o T" option. This is with the latest version of blast (2.2.20 [Feb-08-2009])
If you fomatdb uniprot_sprot.fasta or uniprot_trembl.fasta from the above link, they successfully create the required files but the blast result descriptions are truncated.
NCBI say it's not their fault and EBI don't answer their email.
A quick hack of prepending fake GI numbers to each accession gets the files formatted correctly and allows sequence retrieval but it's not an ideal solution.
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of granjeau at tagc.univ-mrs.fr
> Sent: Tuesday, 19 May 2009 9:39 a.m.
> To: "Cook, Malcolm "@tagc.univ-mrs.fr; " <mec at stowers.org>"@tagc.univ-mrs.fr
> Cc: 'BioPerl List'
> Subject: Re: [Bioperl-l] Uniprot/Swiss accessions?
> May be you try the PICR service at EBI
> or some other ID converter (as for example some Gene Ontology tools) or
> even SRS.
> I think there could be more than one gi per sp (it's not clear to me if
> you are looking at SwissProt or UniProtKB, ie SP+TrEMBL).
> Answer us your solution.
> > 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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