Off topic:How Do I Apply Tfbs Dna Motifs To A Genome?

Question

[Sam]

Possible Duplicate:
Transcription Factor Binding Site Prediction

Hello,

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!