Hello everyone! I would like to ask adiveces for trascription factor binding site prediction.
My co-supervisor asked me to check if a particular human gene promoter has potential binding site for a TF.
I have tried solving out this problem by coding a matlab code based upon information theory but I have found problems with defining a method in order to determine significance level of my result (since Σf*I values don't give any information by themselfs). I have tried one but it has failed to make positive predictions for a consensus site in promoters chosen as "positive controls". Therefore, I would like to change the approach and looking for some online predictors.
Have you got any advice?
I have tried using JASPAR on Genome Broswer but it seems to be not so much convenient since I am not able to download the analysis (and it means I have to check each TF name on the screen, because I cannot use the search function).
Thank you for your support!