PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
Figure 5
Performance of Several Motif-Finding Algorithms on Synthetic Data Prepared as for Figure 3
A total of 250 alignments of S = 5 orthologous intergenic regions of length L = 750 and proximity q = 0.5 were created with three binding sites sampled from each of three different random WMs. The left panel shows how the fraction of predicted sites that match true sites (specificity) depends on the fraction of true sites that are among the predictions (sensitivity) for PhyloGibbs (red), EMnEM (yellow), PhyME (green), PhyloGibbs without phylogeny (light blue), WGibbs (dark blue), and MEME (pink). Dashed lines correspond to two standard errors. The right panel shows the ability of the different algorithms to assess their own reliability. The true specificity is shown as a function of the specificity that the algorithm predicts for the sites that it reports. The black line y = x corresponds to a perfect assessment of the algorithm's reliability.