to evaluate STE12-binding site predictions. We classified predictions as true positive (TP) or false positive (FP) by comparison to the STE12-binding motif, TGAAACA, as determined by (14) . For each sequence, we calculated distance from the known STE12 PWM using a modified local ungapped sequence alignment similar to that in (38) . Alignments were scored as the sum of Pearson's correlation coefficient,