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

[Ryan Golhar]

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Ryan


-----Original Message-----
From: bio_bulletin_board-admin at bioinformatics.org
[mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of
Sebastian Kadener
Sent: Thursday, October 07, 2004 4:08 PM
To: bio_bulletin_board at bioinformatics.org
Subject: [BiO BB] Finding common TF binding sites in promoter regions of
different insect species


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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