title: PhyME: a software tool for finding motifs in sets of orthologous sequences.
abstract: Discovery of transcription factor binding sites is a crucial and challenging problem in bioinformatics. Several computational tools have been developed for this problem, popularly known as the motif-finding problem. PhyME is an ab initio motif-finding algorithm, which finds overrepresented motifs in input sequences while accounting for their evolutionary conservation in orthologs of those sequences. Here, we describe the usage of this algorithm, publicly available as a Linux-based implementation.
authors.affiliation: Department of Computer Science, University of Illinois, USA.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Sinha
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D005075:Biological Evolution; D016415:Sequence Alignment; D012984:Software; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors