Binding site prediction algorithms are generally confounded by several factors: degeneracy in the binding site; the unknown length of the binding site; the relatively large length of promoters; and the inclusion of DSs in the input sets (17, 21, 22) . As a result as few as 10% of predicted positions correspond to biologically functional binding sites (23) . Due, in part, to the low accuracy rate, computational binding site identification has been of limited use (23) . Problems identifying binding sites are further exacerbated in mammalian genomes by larger promoter regions (24) and scarcity of reliable information on co-regulation of genes. Thus, the most demanding test of efficacy for TFBS identification approaches lies in their application to mammalian systems and subsequent validation of predictions.