We find that positional clustering and subsequent selection of frequently recurring nucleotides improved the PPV of the STE12 binding site by at least 37% over Gibbs sampling alone (Figure 2 ). To validate that the above results were not specific to the number of input promoters, the STE12-binding motif, or the particular Gibbs sampling implementation, we repeated the above prediction process for promoters predicted to bind to YAP1, TEC1, HAP4 and YDR026C. We also repeated the analysis replacing the original Gibbs sampling procedure with our own implementation and MotifSampler (44) . In all cases, we found positional clustering significantly improves on results over local optimization procedures alone ( Figure 3 ).