As a preliminary test of the above hypothesis, we applied repeated runs of Gibbs sampling to a set of 51 S.cerevisiae promoters enriched in STE12 binding as identified by wholegenome ChIP-chip experiments (10) . We used positional clustering of 1200 results to identify the most frequently recurring positions (see Methods). Incorporation of additional results did not significantly alter the distribution of results (data not shown). We chose STE12 because it is one of the best studied TFs, with a well known, highly conserved and experimentally well-defined binding motif (10, 43) . The most frequently recurring positions were compared with the known STE12binding motif (40) . We classified predictions into two categories: true positive (TP) if they resemble the experimentally identified STE12-binding motif, and false positive (FP) otherwise (see Methods). Finally, we calculated the positive predictive value PPV as PPV ¼ TP/(TP + FP).