[Bioperl-l] cis-regulatory elements

Chris Fields cjfields at illinois.edu
Sat Oct 16 23:24:32 EDT 2010


Sendu Bala delved into this a bit; you can look at a few of his modules in BioPerl, specifically Bio::DB::TFBS (which is only configured for transfac_pro at the moment).

chris

On Oct 16, 2010, at 3:41 PM, Jun Yin wrote:

> Hi, Illes,
> 
> Sorry I don't know any package in BioPerl predicting TFBS binding motifs. As
> far as I know, neither Bio::Align nor Bio::Assembly has such functions,
> though Bio::SimpleAlign can be used to manipulate your promoter alignment.
> For TFBS prediction, I personally use PScan and TFFind at the moment.
> 
> I am also interested in this question. I will wait for the answer in the
> mail list with you :)
> 
> Cheers,
> Jun Yin
> Ph.D. student in U.C.D.
> 
> Bioinformatics Laboratory
> Conway Institute
> University College Dublin
> 
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Farkas, Illes
> Sent: Saturday, October 16, 2010 12:34 PM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] cis-regulatory elements
> 
> Dear All,
> 
> Which (BioPerl or other) module/algorithm would you recommend for predicting
> cis-regulatory elements (mainly TFBSs) in a variety of organisms? We (= 1
> colleague and I) have looked at
> http://www.nature.com/nbt/journal/v23/n1/full/nbt1053.html so far.
> 
> Thanks,
> Illes
> --
> http://hal.elte.hu/fij
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