Does any one have experience with prediction of transcription factor binding sites ?

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Kumari Sonal Choudhary

I think this would help you http://bip.weizmann.ac.il/toolbox/seq_analysis/promoters.html

if you need help in analysis with these softwares, let me know

Nicky Creux

I really like the set of tools available on the Regulatory sequences analysis tools webpage (http://rsat.ulb.ac.be/) and if you are searching for elements that have been previously identified then TRASFAC is a great database but you need to get a licence for that.