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

Peter biopython at maubp.freeserve.co.uk
Mon Jan 11 05:48:52 EST 2010


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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