Assuming you have a genomic regions from an NGS experiment, aiming to find overrepresented motifs in them, the standard tools are either Homer findMotifsGenome.pl/findMotifs.pl or MEME-CHIP from the MEME suite. Both have extensive documentation and threads covering these can be found on Biostars using the search fucntion.
Thanks everyone guys!
I'll surely try out your tools but my question was little bit different.
I am interested in the understanding if a particular TF motif is enriched in a subset of Gene's promoters.
I've tried to run homer "for an unbiased approach" but I'd like a tool that actually tells me: YES, this particular motif is statistically in your promoters. Any ideas?