Figure 4

Comparison of DEME and MEME on synthetic problems. Each plot shows the accuracy of predicted motifs as measured by the training set PC. Each data point represents the mean (± standard error) PC on 100 independent instantiations of the given problem. Panel a shows results on the FM Random Negative Problem. Panel b shows results for the FM Decoy Motif Problem with zero mutations in the occurrences of the decoy motif as a function of the number of mutations in the target motif sites. Panel c shows results on the FM Variant Motif Problem. The variant motif is Hamming distance four from the target motif and planted instances of the target and variant motifs contain the same number of mutations. Panel d shows results on the width-10 PSFM Impoverished Negative Problem (and width-10 PSFM Random Negative Problem for comparison) as a function of the length of the sequences. In all tests, DEME is run using a positive and negative training set, while MEME is applied to the positive training set only.