Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

ABSTRACT: The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those region

SUBMITTER: Majoros WH 

PROVIDER: S-EPMC3002982 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature