[Bioperl-l] Protein IDs: GenPept and SwissProt

[Jonathan Manning]

Thanks for the help- I had not realised that GenPept accessions and
Swiss-Prot IDs were the same (to some extent)- so O/P/Q prefixes mean
that a genbank file originated from Swiss-Prot?

I have a further question in relation to this. I have noticed that
Swiss-Prot type files in GenBank link to many other protein files in
GenBank, via their gis, presumably because of redundancy. But there's no
link in the other direction. I'd like to be able to read a GenBank
protein file, and tell if it has related listings in Swiss-Prot- is this
possible? I have previously had some success using keywords with a
Bio::DB::Query::GenBank object, with quite a diverse range of queries.
Unfortunately neither this, nor the NCBI web query interface seems to
'see' GIs as keywords to search for in the database, and only bring up
the sequence that the GI belongs to- not other records in which it is
mentioned.

Any more help is much appreciated!

Jon  

On Wed, 2004-05-05 at 12:02, Jason Stajich wrote:
> Though not every genpept (primary data) will have a sp id (curated data).
> 
> This file can give you the accession -> sp mapping for those which are
> mapped.
> ftp://ftp.expasy.ch/databases/swiss-prot/release/acindex.txt
> 
> -jason
> On Wed, 5 May 2004, Jonathan Manning wrote:
> 
> > Hi All,
> >
> > Is there an easy way to relate/convert protein GenBank (GenPept) IDs to
> > a swiss-prot accession? I thought maybe SeqHound could be useful there,
> > but can't see what I need.
> >
> > Cheers,
> >
> > Jon
> >
> > _______________________________________________
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> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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