[ensembl-dev] Check if a gene has a pseudogene

[Ryan Giuliany]

Ok, thanks for the help!

Ryan
________________________________________
From: dev-bounces at ensembl.org [dev-bounces at ensembl.org] On Behalf Of Javier Herrero [jherrero at ebi.ac.uk]
Sent: Wednesday, August 10, 2011 6:40 AM
To: dev at ensembl.org
Subject: Re: [ensembl-dev] Check if a gene has a pseudogene

Hi Ryan

There is no direct link from a pseudogene to its parent known gene (assuming
this exists, that is). Your best option is to align your pseudogenes of
interest to all coding genes in that species.

I hope this helps

Javier

On Monday 08 Aug 2011 19:40:10 Ryan Giuliany wrote:
> Hi,
>
> I think you're correct. To be more precise:
>
> A gene either is or is not a pseudogene, but in the case where it *is* a
> pseudogene, in many cases the pseudogene was created via a gene
> duplication event of another, possibly protein coding, gene.  I suppose my
> questions would be better worded as "is there any way to check if a gene
> is a parent of a known pseudogene?".
>
> Ryan
> ________________________________________
> From: carandraug at gmail.com [carandraug at gmail.com] On Behalf Of Carnë Draug
> [carandraug+dev at gmail.com] Sent: Monday, August 08, 2011 11:31 AM
> To: Ryan Giuliany
> Cc: dev at ensembl.org
> Subject: Re: [ensembl-dev] Check if a gene has a pseudogene
>
> On 8 August 2011 19:06, Ryan Giuliany <rgiuliany at bccrc.ca> wrote:
> > Hi,
> >
> > Is it possible to check if a gene has (not is) a known pseudogene?  I've
> > been sifting through the docs, and can't find anything.
> >
> > Thanks!
> > Ryan
>
> Hi Ryan
>
> I believe a gene either is, or is not, a pseudo gene. Do you mean to
> ask if a gene has (or has not), a non-coding transcript?
>
> Carnë
>
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--
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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