Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes.

ABSTRACT: Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindered our understanding of many important biological processes. In this article, we describe a novel algorithm for genome-wide de novo prediction of CRBSs with high accuracy. We designed our algorithm to circumvent three identified difficulties for CRBS prediction using comparative genomics principles based on a new method for the selection of reference genomes, a new metric for measuring the similarity of CRBSs, and a new graph clustering procedure. When operon structures are cor

SUBMITTER: Zhang S 

PROVIDER: S-EPMC2691844 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature