[Bioperl-l] Database Retrieval
bix at sendu.me.uk
Mon Aug 7 11:51:19 EDT 2006
Rick Scavetta wrote:
> Hello Programmers,
> I have a list of mouse GeneIDs for which I have extracted the RefSeqs for.
> With these accession numbers I want to know what are the three closest
> upstream and downstream genes (and orientation, if possible) to my gene of
> interest. Is these some way of finding this out? Any suggestions?
One possible way would be with the Ensembl Perl API:
You'd get a gene or transcript adapator and use
Then probably your slice adaptor would be used to get the up and down
stream regions and iirc there's some easy way to ask for all the genes
in a slice.
Sean's solution (use UCSC) seems a lot easier, and since you just want a
list of names as a result, not bioperl objects, I'd go for that.
Actually, would there be any interest in a bioperl interface to the UCSC
tables? It could probably be done using their DAS server, and end up as
a very easy-to-use alternative to the Ensembl API for limited or one-off
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