[Bioperl-l] Retrieve Sequence from Ensembl gene id

Chris Fields cjfields at illinois.edu
Thu Sep 30 11:16:45 EDT 2010


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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