MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders

Locating transcription factor binding sites (motifs) is a key step in understanding gene regulation. Based on Tompa's benchmark study, the performance of current de novo motif finders is far from satisfactory (with sensitivity

In this article, we identify several key observations on how to utilize the results from individual finders and design a novel ensemble method, MotifVoter, to predict the motifs and binding sites. Evaluations on 186 datasets show that MotifVoter can locate more than 95% of the binding sites found by its component motif finders. In terms of sensitivity and precision, MotifVoter outperforms stand-alone motif finders and ensemble methods significantly on Tompa's benchmark, Escherichia coli, and ChIP-Chip datasets. MotifVoter is available online via a web server with several biologist-friendly features.