title: FootPrinter3: phylogenetic footprinting in partially alignable sequences.
abstract: FootPrinter3 is a web server for predicting transcription factor binding sites by using phylogenetic footprinting. Until now, phylogenetic footprinting approaches have been based either on multiple alignment analysis (e.g. PhyloVista, PhastCons), or on motif-discovery algorithms (e.g. FootPrinter2). FootPrinter3 integrates these two approaches, making use of local multiple sequence alignment blocks when those are available and reliable, but also allowing finding motifs in unalignable regions. The result is a set of predictions that joins the advantages of alignment-based methods (good specificity) to those of motif-based methods (good sensitivity, even in the presence of highly diverged species). FootPrinter3 is thus a tool of choice to exploit the wealth of vertebrate genomes being sequenced, as it allows taking full advantage of the sequences of highly diverged species (e.g. chicken, zebrafish), as well as those of more closely related species (e.g. mammals). The FootPrinter3 web server is available at: http://www.mcb.mcgill.ca/~blanchem/FootPrinter3.
authors.affiliation: McGill Centre for Bioinformatics, 3775 University St, Montréal, Québec, Canada, H3A 2B4.
authors.forename: Fei
authors.initials: F
authors.lastname: Fang
authors.forename: Mathieu
authors.initials: M
authors.lastname: Blanchette
mesh_terms: D000818:Animals; D001665:Binding Sites; D018983:DNA Footprinting / Q000379:methods*; D023281:Genomics / Q000379:methods*; D020407:Internet; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment / Q000379:methods*; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors