[Bioperl-l] Bio:DB:SeqFeature - MySql - Java

Bernd Jagla bernd.jagla at pasteur.fr
Mon Jan 11 05:53:20 EST 2010


I am using bp_seqfeature_load.pl to load my features. That is using
Bio:DB:SeqFeature(Store) and MySql as a backend... That's all I
understood...

B

> -----Original Message-----
> From: p.j.a.cock at googlemail.com [mailto:p.j.a.cock at googlemail.com] On
> Behalf Of Peter
> Sent: Monday, January 11, 2010 11:49 AM
> To: Bernd Jagla
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio:DB:SeqFeature - MySql - Java
> 
> On Mon, Jan 11, 2010 at 10:11 AM, Bernd Jagla <bernd.jagla at pasteur.fr>
> wrote:
> > Hi,
> >
> > First off, I am not sure if this is supposed to be addressed to the
> Bioperl
> > or Gbrowse mailing list, so apologies if this is the wrong list and
> please
> > let me know.
> >
> > I am writing a program in Java that needs to access genome annotation
> data.
> > Since I am using Gbrowse already I was thinking that I could combine
> both
> > approaches making life eventually easier for me. I am mainly interested
> in
> > getting a gene/feature name for a given position. The position is stored
> in
> > the feature table and through linking typelist, locationlist, (maybe
> > sequence), and feature I can get all the information I need.
> Unfortunately
> > it seems that the feature name is stored in the object blog of the
> feature
> > table.
> 
> How are you storing the data in Gbrowse? There are several back ends,
> and this will make a big difference for accessing the raw data.
> 
> One option would be to use Gbrowse with BioSQL as the backend.
> You can then use BioJava (or BioPerl, or BioPython, etc) to access the
> database. The only downside is Gbrowse isn't working 100% on top
> of BioSQL right now (I'd like to see this fixed, but I don't know Perl).
> There is an open bug on this [ gmod-Bugs-2168597 ].
> 
> Peter




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