[Bioperl-l] about gene "boundaries"

Scott Cain scott at scottcain.net
Wed Apr 28 10:19:27 EDT 2010

Hi Dimitar,

It would be easy if your local database is one that bioperl talks to:
Bio::DB::GFF, Bio::DB::SeqFeature::Store, and with slightly more work,
BioSQL or Chado.  If not, you'd have to write your own adaptor for
your database that would issue the queries and package the results up
as Bio::Seq or Bio::SeqFeature objects (whichever is appropriate for
your use).


On Wed, Apr 28, 2010 at 9:17 AM, Dimitar Kenanov
<dimitark at bii.a-star.edu.sg> wrote:
> Hello guys,
> i have a question about gene "boundaries". Is there some module in BioPerl
> which can help me extract the DNA sequence from a genomic DB (from specific
> chromosome). I have my human genome in a local DB and some "from-to" data
> sets corresponding to different chromosomes. So i want to get the DNA seqs
> for these from-to's. I know i can do that the normal way but if there is a
> way to do it with BioPerl it will be more consistent with the rest of the
> code.
> Thanks for any tips :)
> Cheers
> Dimitar
> --
> Dimitar Kenanov
> Postdoctoral research fellow
> Protein Sequence Analysis Group
> Bioinformatics Institute
> A*STAR, Singapore
> email: dimitark at bii.a-star.edu.sg
> tel: +65 6478 8514
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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