Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

ABSTRACT: Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs) and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs) and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational

SUBMITTER: He X 

PROVIDER: S-EPMC2657044 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature