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

Chris Fields cjfields at illinois.edu
Thu Sep 18 17:48:26 EDT 2008


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/software/scripts/affyprobeset2ensg/
>
> 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  It may be outdated due to changes in  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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