I'm new to gene regulatory site analysis. I have a promoter/enhancer sequence from multiple species (human, mouse, rat, a species not yet have a genome draft) and would like to align them and look for transcription factor binding sites. I can align sequences using multiple programs but am having a hard time finding one that will also allow you to do a search on the aligned sequences to find transcription factor binding site based on available TFmatrices. Does anyone have suggestions on a program that can perform such tasks? Reply is greatly appreciated.
Conreal allows such analysis for pairwise alignments:
http://conreal.niob.knaw.nl/index.html
There are probably newer, better options and I will be interested in other answers to your question!
The Genomatix software package will do this easily enough, however it is not readily available. You may find someone at your institution that has a paid subscription.
Mai, if you want to give the Genomatix software package a try, you can get a two weeks free trial at the link below. You can use the DialignTF program from the GeneRegulation package to align multiple sequences plus identify TF binding site motifs.
http://www.genomatix.de/cgi-bin/UMapps/register.pl
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