[BiO BB] Re: Finding common TF binding sites in promoter regions of different insect species

William Thompson thompson at wadsworth.org
Fri Oct 8 13:11:34 EDT 2004

There are a number of good tools on the web for finding TFBS: meme which you 
mentioned and Gibbs sampling based tools 
http://bayesweb.wadsworth.org/gibbs/gibbs.html and 
http://www.esat.kuleuven.ac.be/~thijs/Work/MotifSampler.html. They work best 
when the sequences that you are searching are regulatory regions from 
co-regulated genes in a single species or from orthologous genes from related 
species. It sounds like you have already regions from related species. You might 
want to check out http://bayesweb.wadsworth.org/web_help.PF.html and 
http://bayesweb.wadsworth.org/web_help_text.CE.html. There are some general 
guidelines there that might be helpful. 

Bill Thompson, PhD
Bioinformatics Center
NYS Department of Health
Center for Medical Science, rm 2006
150 New Scotland Avenue
Albany, New York 12208
(518) 486-7882
thompson at wdsworth.org

> Dear list members,
> I am trying to find TF binding sites (not ones that are currently known and in
> databases) in the promoter regions of at least four species of insects (the 3
> sequenced drosophila and anopheles).  I have used meme for this already but
> the results that I got weren't so good.
> I was thinking of performing some kind of multiple local alignment to find 
> regulatory elements among the promoters but I wasn't sure how to go about
> doing this.  
> If anyone has any suggestions on how to find TF binding sites in promoters, I
> would be very interested in hearing them.  Thank you in advance.
> Sebastian
> -- 
> Sebastian Kadener 
> Rosbash laboratory 
> Dept. of Biology, MS008 
> Brandeis University/HHMI 781 736 3163 tel 
> 415 South St. 781 736 3164 fax 
> Waltham, MA  02454 skadener at brandeis.edu 

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