[Bioperl-l] How to retrieve info about whether a Seq is a partial or complete CDS

Christopher Goddard cgoddard at flmnh.ufl.edu
Wed Jan 28 17:31:48 EST 2009


Thank you.  I was finally able to figure it out.  I'm a bit embarrassed 
to say this, but the problem was that I was not specifying the database 
to query when I did the get_Stream_by_query() call, and it was returning 
results from a database without that coding sequence completion 
information in the definition.

Chris



Jason Stajich wrote:
> where is the information in the genbank record (as a text file)?
> DEFINITION  ?
>
> -jason
>
> On Jan 28, 2009, at 10:02 AM, Christopher Goddard wrote:
>
>> I need to determine if a Bio::Seq object returned from GenBank by a 
>> Bio::DB::GenBank->get_Stream_by_query() call is a partial or complete 
>> coding sequence.  This information is given in the description for a 
>> sequence when performing a search on Entrez.  However, using the 
>> method desc() for the sequences returned doesn't relay this 
>> information, at least not all of the time.  If someone could point me 
>> in the right direction on where I could retrieve this information I 
>> would be really appreciative.
>>
>> Thanks
>> Chris
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org <mailto:Bioperl-l at lists.open-bio.org>
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Jason Stajich
> jason at bioperl.org <mailto:jason at bioperl.org>
>
>
>

-- 
Christopher Goddard
IT Expert, Informatics
Florida Museum of Natural History
University of Florida
Gainesville, FL  32611
phone:  352-273-1823 



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