CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing.

ABSTRACT: Functional turnover of transcription factor binding sites (TFBSs), such as whole-motif loss or gain, are common events during genome evolution. Conventional probabilistic phylogenetic shadowing methods model the evolution of genomes only at nucleotide level, and lack the ability to capture the evolutionary dynamics of functional turnover of aligned sequence entities. As a result, comparative genomic search of non-conserved motifs across evolutionarily related taxa remains a difficult challenge, especially in higher eukaryotes, where the cis-regulatory regions containing motifs can be long and divergent; existing methods rely heavily on specialized pattern-driven heuristic search or sampling algorithms, which can be difficult to generalize and hard to interpret based on phylogenetic princip

SUBMITTER: Ray P 

PROVIDER: S-EPMC2396503 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature