Performance on site prediction using PhyloGibbs-MP. The performance of the motif-finder PhyloGibbs-MP when various programs are used to align its input data. Upstream sequence for 205 genes from S. cerevisiae and up to 4 orthologues are aligned, and PhyloGibbs-MP is run on those alignments. Predictions are compared with known regulatory sites from the SCPD database. The figure shows the fraction of PhyloGibbs-MP predictions that overlap with SCPD sites ("precision") as a function of the fraction of SCPD sites retrieved by PhyloGibbs-MP ("sensitivity"). Sensitivity is varied by changing the cutoff for PhyloGibbs-MP's significance assessment.