[Bioperl-l] cis-regulatory elements

Jun Yin jun.yin at ucd.ie
Sat Oct 16 16:41:37 EDT 2010


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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