Performance comparison of algorithms for finding transcription factor binding sites

We compare the accuracy of three motif-finding algorithms for the discovery of novel transcription factor binding sites among co-regulated genes. One of the algorithms (YMF) uses a motif model tailored for binding sites and an enumerative search of the motif space, while the other two (MEME and AlignACE) use a more general motif model and local search techniques. The comparison is done on synthetic data with planted motifs, as well as on real data sets of co-regulated genes from the yeast S. cerevisiae. More often than not, the enumerative algorithm is found to be more accurate than the other two on the yeast data sets, though there is a noticeable exclusivity in the accuracy of the different algorithms. The experiments on synthetic data reveal, not surprisingly, that each algorithm outperforms the others when motifs are planted according to its motif model.