There are numerous tools to execute this function; however, the utility of this analytical approach is extremely limited for the following reasons:

1) motifs occur in greater frequencies than the observed binding for their cognate transcription factors in any given genome (i.e. not all motifs are functional in terms of factor recruitment).

2) transcription factors act at a distance. Therefore, even when a motif does recruit its cognate factor, there is not a 1:1 relationship between the most proximal gene and gene targeted for regulation by that motif, if that motif serves any regulatory function at all.

3) occurrence of a single motif or binding site is rarely enough to confer dependence of gene expression on a particular factor (while there are exceptions, it is generally more informative if your regulatory motif is present in several copies near a candidate locus)

So be careful in trying to read too deeply into these motif-based analyses, unless you can apply some other constraints to enrich for functional relationships between your motif of interest and potential target genes (for example, gene expression changes in knockdown, knockout, or induced expression cell lines).

One commonly used tool is FIMO at the MEME site:

http://meme.nbcr.net/meme/cgi-bin/fimo.cgi

Thanks alot