Phylogeny based discovery of regulatory elements

Background: Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences. Results: We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Jason Gertz, Justin C. Fay, Barak A. Cohen
• Keywords: BMCBI 2006, Functional Dna, Sequences, Transcription Factor