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

[Fei Li]

Hi, Sebastian, 
 
You can also check the webpages of Michael Q Zhang in CSHL, http://rulai.cshl.edu/ , he did lots of work on TFBS 

alignment between three drosophila species provide little useful informations. Because they are very  close in phylogeny.  Maybe, alignment between drosophila and anopheles will be better. 

   I got this from Micahel. Finding motif by sequnce alignment will largely rely on the relationship between speices you selected.  For more information, please directly contact Michael directly, a very kind PI in cshl. 

Best

Fei

Sebastian Kadener <skadener at brandeis.edu> wrote:

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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-------------------------------------------------
Fei Li, PhD, Postdoc fellow
Institute of Bioinformatics
MOE key laboratory of Bioinformatics
Tsinghua University
Beijing, 100084
China
Tel:0086-10-62782877
Fax:0086-10-62786911
E-mail: flee at tsinghua.edu.cn
Homepages:http://166.111.30.65/member/~lifei/


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