[BioPython] splice variants in GenBank/Entrez

[Albert Krewinkel]

Hi Steve,

On Sun, Jun 08, 2008 at 10:21:50PM -0700, C. G. wrote:
> 
> I've been using BioPython for a few projects the last
> two months to process BLAST results but now I need to
> take those results and determine which of them have
> known splice variants. By "known" I mean those that
> have annotations contained in a database that indicate
> they have (or are) splice variants.

Depending on which organism you are looking at, you might want to use
the Ensembl genome database.  There is no biopython interface, but you
can use the jython interface from their website (at least they once
had one, I didn't check if that's still the case).  Otherwise you
might have to use perl or java packages for that.

Another good resource for this is the Alternative Splicing Database:
http://www.ebi.ac.uk/asd/

Hope that helps,

Albert


-- 
Albert Krewinkel <krewink (at) inb.uni-luebeck.de>
University of Luebeck, Institute for Neuro- and Bioinformatics
http://www.inb.uni-luebeck.de/~krewink/