title: Detecting regulatory sites using PhyloGibbs.
abstract: PhyloGibbs is a program that uses Gibbs sampling to predict putative binding sites for transcription factors in DNA. It has two notable advances over previous algorithms for this task: it handles phylogenetically related sequence systematically, and it evaluates the significance of each predicted site via statistical sampling. In this article, we explain how to use PhyloGibbs effectively. We describe the essential command-line options in detail, and discuss other considerations that arise in practical situations.
authors.affiliation: Institute of Mathematical Sciences, India.
authors.forename: Rahul
authors.initials: R
authors.lastname: Siddharthan
authors.forename: Erik
authors.initials: E
authors.lastname: van Nimwegen
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D030541:Databases, Genetic; D020407:Internet; D008969:Molecular Sequence Data; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid; D014584:User-Computer Interface
chemical_list: D004247:DNA