PRISM finds degenerate motifs that are statistically over-represented in your group of genes relative to their frequency of occurrence in the genome. PRISM works on the output of BEAM, an approach that works well if the binding sites are 5-9 nucleotides long. For detail see our paper: Carson* JM, Chakravarty* A, Khetani RS, and Gross RH. "Bounded search for de novo identification of degenerate cis-regulatory elements." BMC Bioinformatics, 2006 May 15; 7(1):254.