[Bioperl-l] Converting EnSeMBL Probe names to Gene Symbol with Bioperl

Cook, Malcolm MEC at stowers-institute.org
Fri Sep 19 09:09:00 EDT 2008


Chris is right- the Ensembl perl API works fine. If you care to go this route and want to crib the code, you will see that my script has a commented out implementation using Ensembl perl API - it suffered from being MUCH TOO SLOOOOOOOOOO - accessing the tables directly was MUCH faster (unpublished correspondance with self)

However, the API is much more likely to be backwards compatible in the face of database schema changes at Ensembl....

Malcolm Cook

-----Original Message-----
From: Chris Fields [mailto:cjfields at illinois.edu]
Sent: Thursday, September 18, 2008 4:48 PM
To: Cook, Malcolm
Cc: 'Gundala Viswanath'; 'bioperl-l at lists.open-bio.org'
Subject: Re: [Bioperl-l] Converting EnSeMBL Probe names to Gene Symbol with Bioperl

You can probably use the Ensembl perl API alone or in combination with bioperl.  I'm not sure it is working with the latest code (bioperl- live), but it's worth a try:

http://www.ensembl.org/info/using/api/core/core_tutorial.html
http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences#Using_the_Perl_API_at_ENSEMBL

chris

On Sep 18, 2008, at 4:20 PM, Cook, Malcolm wrote:

> Gundala,
>
> Here is an option - if you want a script...
>
> http://research.stowers-institute.org/mec/softyware/scripts/affyprobese
> t2ensg/
>
> It is not bioperl.   It is perl.  It uses DBI to query the ensembl
> MySQL database using SQL.  It may be outdated due to changes in
> Ensembl schema.
>
> Good luck,
>
> Malcolm Cook
> Stowers Institute for Medical Research - Kansas City, Missouri
>
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org
> ] On Behalf Of Gundala Viswanath
> Sent: Thursday, September 18, 2008 3:52 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Converting EnSeMBL Probe names to Gene Symbol
> with Bioperl
>
> Dear all,
>
> Is there a way I can convert such EnSeMBL probe names into Gene Symbol
> with BioPerl?
>
> ENSG00000000003_at
> ENSG00000000005_at
> ENSG00000000419_at
> ENSG00000000457_at
> ENSG00000000460_at
> ENSG00000000938_at
> ENSG00000000971_at
> ENSG00000001036_at
> ENSG00000001084_at
> ENSG00000001167_at
> ENSG00000001461_at
> ENSG00000001497_at
> ENSG00000001561_at
> ... etc ...
>
> Or perhaps there is a flat file for conversion?
>
>
>
> - Gundala Viswanath
> Jakarta - Indonesia
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign







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