[Bioperl-l] bioperl version for ensembl Was: Retrieve Sequence from Ensembl gene id

Albert Vilella avilella at gmail.com
Tue Oct 5 06:00:28 EDT 2010


I also tested bioperl 1.6.1 for some scripting with the Ensembl API, and it
produces a few warnings here and there, but it doesn't break anything
obvious...

On Thu, Sep 30, 2010 at 4:16 PM, Chris Fields <cjfields at illinois.edu> wrote:

> On Sep 30, 2010, at 8:36 AM, Jun Yin wrote:
>
> > Hi, Chirag,
> >
> > BioPerl does not have any module to retrieve data from Ensembl. But
> Ensembl
> > provides a BioPerl-like interface on that function.
>
> Actually, BioPerl does have Bio::Tools::Run::Ensembl, which was submitted
> by Sendu Bala a few years back.  I think it stills works rather well, at
> least tests pass.  You might get more out of using the Ensembl API directly
> as Jun states though, YMMV.
>
> BTW, the ensembl API also works with the latest bioperl code, regardless
> what the Ensembl website says (e.g. they only support v1.2.3).  Haven't
> heard more about whether this discrepancy was supposed to be addressed at
> some point.
>
> chris
>
> > You can visit Ensembl's website on how to use that module:
> > http://www.ensembl.org/info/data/api.html
> >
> > Cheers,
> > Jun Yin
> > Ph.D. student in U.C.D.
> >
> > Bioinformatics Laboratory
> > Conway Institute
> > University College Dublin
> >
> >
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org
> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of chirag matkar
> > Sent: Thursday, September 30, 2010 1:21 PM
> > To: bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Retrieve Sequence from Ensembl gene id
> >
> > Hello all,
> > Is there any module to fetch dna sequence data from ensemble gene id?
> >
> > --
> > Regards,
> > Chirag Matkar
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