[Bioperl-l] Refseq Hits

[shalabh sharma]

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
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>
>