[Bioperl-l] Refseq Hits

[Smithies, Russell]

The identifiers are separated by a Ctrl-A char ("\001") in the original non-redundant fasta header so you should be able to split them up again - assuming BioPerl didn't munge them.

--Russell

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of shalabh sharma
> Sent: Wednesday, 3 June 2009 3:16 a.m.
> To: Jonathan Crabtree
> Cc: bioperl-l
> Subject: Re: [Bioperl-l] Refseq Hits
> 
> Hi Jonathan,                  Your information is really helpful. Thanks a
> lot.
> 
> -Shalabh
> 
> 
> On Tue, Jun 2, 2009 at 11:04 AM, Jonathan Crabtree <
> jonathancrabtree at gmail.com> wrote:
> 
> >
> > Hi Shalabh-
> >
> > I believe RefSeq is a non-redundant database, in which sequence entries
> > with identical sequences are merged and their descriptions are concatenated
> > in the FASTA defline.  If you look up the two accession numbers/gi numbers
> > from your search results I think you'll see that both are valid matches
> > because their polypeptide sequences are identical:
> >
> > http://www.ncbi.nlm.nih.gov/protein/71082715
> > http://www.ncbi.nlm.nih.gov/protein/91762865
> >
> > You're just getting a single match with two descriptions instead of two
> > matches with one description, but the sequence is the same and so, therefore
> > are the blast alignments.
> >
> > Jonathan
> >
> > On Tue, Jun 2, 2009 at 10:44 AM, shalabh sharma <shalabh.sharma7 at gmail.com
> > > wrote:
> >
> >> Hi All,
> >>          This is not really a bioperl query, but i am really confused and
> >> need some help.
> >> I blasted some sequences against refseq database (locally). After parsing
> >> the blast result what i noticed that some description fields contain two
> >> hit
> >> names like:
> >> hit_name ->    gi|71082715|ref|YP_265434.1|
> >> Description -> ubiquitin binding protein [Candidatus Pelagibacter ubique
> >> HTCC1062] gi|91762865|ref|ZP_01264830.1| possible ubiquitin binding
> >> protein
> >> [Candidatus Pelagibacter ubique HTCC1002]
> >>
> >> So besides giving me description for hit_name (HTCC 1062) its also giving
> >> me
> >> HTCC 1002.
> >> I will really appreciate if someone can help me out.
> >>
> >> Thanks
> >> Shalabh
> >> _________________________________________________
> >> Shalabh Sharma
> >> Scientific Computing Professional Associate
> >> Department of Marine Sciences
> >> University of Georgia
> >> Athens, GA 30602-3636
> >>
> >> phone: 706-542-0341
> >> email: ssharmai at uga.edu
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >
> >
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