PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
Figure 3
Performance of PhyloGibbs and Non-Phylo Motif-Finding Algorithms on Alignments of Orthologous Intergenic Regions as a Function of the Evolutionary Proximity of the Orthologs and the Quality of the WM
PhyloGibbs with phylogeny (red), PhyloGibbs in non-phylo mode (light blue), WGibbs (dark blue), and MEME (pink) were run on alignments of S = 5 intergenic regions of length L = 500, each at a proximity q to the common ancestor and each containing s = 4 binding sites from a single WM of width w = 10. In the upper left panel, WMs had polarization p = 0.6, in the upper right p = 0.75, in the lower left p = 0.9, and in the lower right random WMs (drawn uniformly from the simplex) were used. The solid lines show the average overlaps between the predicted sites and the real sites, and the dotted lines show two standard errors (estimated from 50 different datasets generated with equal parameters for each data point).