Performance of six motif finding tools on our compendium of metazoan target sets. (A) Success rates for three PWM divergence cutoffs, indicated by different shades of gray. The light-gray boxes on top of the Amadeus bars show the improved success rates when using the binned enrichment score (instead of the HG score; see Methods). Success rates for other PWM similarity measures and cutoffs are shown in Supplemental Figure 4. (B) Running times in logarithmic scale for the TF target-sets (AlignACE and MEME did not finish within 48 h on several sets). Trawler is a web-based tool so we could not measure its running time. For full results, see Supplemental Table 1 and http://acgt.cs.tau.ac.il/amadeus. A detailed comparison of all tested tools is given in Supplemental Table 2.
