Transcription Factor Binding Site Prediction
I am interested in learning how to apply TFBS matrices (such as those available from TRANSFAC and JASPAR) to the HG18 and HG19 genomes. Is there a tool out there to accomplish this? Is there some well-established threshold to set when calculating scores? Are these matrices typically applied to the regions upstream of known transcripts/genes? If not, where else?
Thank you in advance for your help!