title: Using the Gibbs Motif Sampler for phylogenetic footprinting.
abstract: The Gibbs Motif Sampler (Gibbs) is a software package used to predict conserved elements in biopolymer sequences. Although the software can be used to locate conserved motifs in protein sequences, its most common use is the prediction of transcription factor binding sites (TFBSs) in promoters upstream of gene sequences. We will describe approaches that use Gibbs to locate TFBSs in a collection of orthologous nucleotide sequences, i.e., phylogenetic footprinting. To illustrate this technique, we present examples that use Gibbs to detect binding sites for the transcription factor LexA in orthologous sequence data from representative species belonging to two different proteobacterial divisions.
authors.affiliation: Center for Computational Molecular Biology, Brown Unversity.
authors.forename: William
authors.initials: W
authors.lastname: Thompson
authors.forename: Sean
authors.initials: S
authors.lastname: Conlan
authors.forename: Lee Ann
authors.initials: LA
authors.lastname: McCue
authors.forename: Charles E
authors.initials: CE
authors.lastname: Lawrence
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D005786:Gene Expression Regulation; D010802:Phylogeny; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors