[Bioperl-l] Bioperl module for upstream/downstream genes ?

[Ewan Birney]

On Mon, 24 Mar 2003, Charles A. Alexander wrote:

> Hello
>
> I was wondering if anybody knows of a module, that given a specific gene
> name or coordinate can find the first transcription start site for a
> (preferably Refseq) gene upstream/downstream from the initial gene location.

I am not 100% sure what you want here, but almost certainly this is
answerable inside Ensembl. Two basic options:

  (a) use Ensmart - go to Ensembl, click on human, click on data mining,
then either pick a particular gene or a chromosome or whatever (in filter)
and then in output choose the start,end and/or use the structure (which
means gene structure here) option to get exon coordinates out.

  (b) use the Ensembl API, which is (loosely) based around Bioperl. Go to
Ensembl, click on documentation, click on tutorial. Notice you can work
directly against our internet accessible database, kaka.sanger.ac.uk so
you don't need to download anything, though if you start doing anything
complex, you might want the DB local.





>
> I looked through the Bioperl documentation and it wasn't obvious if anything
> like this exists for the Santa Cruz Genome Browser or Ensembl based
> annotations.
>
> Thanks in advance,
>
> Charles Alexander
> --
> Charles Alexander, Bioinformatics Specialist
> 615 322-0855 (Day)/615 343-8619 (Fax)
> charles.alexander at vanderbilt.edu
>
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