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

[Sebastian Kadener]

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