[Bioperl-l] Refseq and Splice Variants

Ewan Birney birney at ebi.ac.uk
Tue Mar 15 03:52:22 EST 2005

Peter J Stogios wrote:
> Hi,
> I am wondering if there is a way of easily identifying Refseq sequences 
> that are splice variants of the same gene.  If a gene has multiple 
> splice products that are supported by experimental evidence, they get 
> their own Refseq identifier, but there is no explicit reference to the 
> underlying gene they came from (outside of the identifier line).
> What I am trying to do is group sets of Refseq sequences in FASTA format 
> into sets of splice variants of the same gene.  Does anyone know of a 
> way, using Bioperl, that I can accomplish this?

One way to handle this is to use Ensembl's genes/transcript links, and
each transcript is linked to its RefSeq if it has one.

The easiest way to do this is via Mart.

Go to Ensembl, Click on Mart, Click on Human and Ensembl Genes,
in filter make sure you don't have a genome filter on, optional
select "Genes with RefSeq IDs" if you are only interested in the
RefSeq subset, then click
on next, and in Output, select

Ensembl Gene-ID, Ensembl Transcript-ID, RefSeq-ID

this will give you the 3 way table to use (you can get this as tab

On route, you can note in filter how many different constraints
you can make on this :)

> Thanks,
> ~
> Peter J Stogios
> Ph.D. candidate, Privé Lab
> Dept. of Medical Biophysics, University of Toronto
> Ontario Cancer Institute, Princess Margaret Hospital
> e: pstogios at uhnres.utoronto.ca
> w: http://xtal.uhnres.utoronto.ca/prive
> p: (416) 946-4501x3280
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