[Bioperl-l] Database Retrieval

Sendu Bala 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:
http://www.ensembl.org/info/software/core/core_tutorial.html

You'd get a gene or transcript adapator and use
fetch_all_by_external_name() iirc.

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 
queries.


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