[Bioperl-l] Get genes/annotations associated with a probe

Jason Stajich jason at bioperl.org
Mon May 26 16:23:06 EDT 2008


As always, what species are you talking about; not everyone works on  
human only?

If human I would suggest using EnsemblMart or Ensembl API for this  
kind of data.  http://biomart.org/

There is a perl API in Ensembl which can be used to query this sort  
of thing.  It will probably be easier to just download the EnsMart  
full set of annotations with genomic locations included and then you  
can do an overlap lookup - or load into Bio::DB::GFF to get the  
transcript name and overlap lookup.

-jason
On May 26, 2008, at 1:18 PM, Arkady wrote:

> Hi everyone,
>
> I've got a list of genomic positions (e.g., the coordinates used by  
> UCSC)
> for transcribed fragments from a microarray. Is there a simple way  
> to get a
> list of annotations for those regions using bioperl? e.g., every  
> annotation
> that spans the entire length of the transfrag, or 80% of it; or  
> annotations
> that overlap the transfrag?
>
> Thanks in advance!
>
> Cheers,
> John Woods
>
> --
> Institute for Cellular and Molecular Biology
> The University of Texas at Austin
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