Figure 3. Evaluation of motif discovery tools on yeast and metazoan benchmarks.

(a) Summary of the success rates of the tested algorithms on yeast and metazoan target sets. AMD and eight other tools were applied to the yeast and metazoan target sets. For each tool on each target set, the three top-scoring motifs were compared to the expected motif by CompareACE and the motif with the highest score was selected as the identified motif. Using a CompareACE score cutoff of 0.65, 0.75 or 0.85, the success rates of each tool on the yeast and metazoan target-set benchmarks were calculated. The number and percentage of motifs correctly identified by each tool are indicated. (b) Measurements of motif-level prediction accuracy of different tools on yeast and metazoan target sets.