Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes.

ABSTRACT: We present a new computational method for solving a classical problem, the identification problem of cis-regulatory motifs in a given set of promoter sequences, based on one key new idea. Instead of scoring candidate motifs individually like in all the existing motif-finding programs, our method scores groups of candidate motifs with similar sequences, called motif closures, using a P-value, which has substantially improved the prediction reliability over the existing methods. Our new P-value scoring scheme is sequence length independent, hence allowing direct comparisons among predicted motifs with different lengths on the same footing. We have implemented this method as a Motif Recognition Computer (MREC) program, and have extensively tested MREC on both simulated and biological data fro

SUBMITTER: Li G 

PROVIDER: S-EPMC2811016 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature