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

[Charles Alexander]

on 3/25/03 3:25 AM, Ewan Birney at birney at ebi.ac.uk wrote:

> 
> 
> 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.
> 

Many thanks, Ewan.

Charles
> 
> 
> 
> 
>> 
>> 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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> 
>