[Bioperl-l] about gene "boundaries"

Chris Fields cjfields at illinois.edu
Wed Apr 28 11:10:40 EDT 2010

By local DB, do you mean a BioPerl-based local DB?  Or is it something else?  This is a bit vague.

On the BioPerl side I suggest looking into Bio::DB::SeqFeature::Store for storing and querying genome information (it does exactly what you want if the proper information is loaded), or maybe the Ensembl Perl API, which can be used with a local or remote Ensembl setup.  Beyond that you'll need to be more specific.


On Apr 28, 2010, at 8:17 AM, Dimitar Kenanov 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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