title: ConSite: web-based prediction of regulatory elements using cross-species comparison.
abstract: ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/www.phylofoot.org/consite.
authors.affiliation: Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius väg 35, s-17177 Stockholm, Sweden.
authors.forename: Albin
authors.initials: A
authors.lastname: Sandelin
authors.forename: Wyeth W
authors.initials: WW
authors.lastname: Wasserman
authors.forename: Boris
authors.initials: B
authors.lastname: Lenhard
mesh_terms: D000818:Animals; D001665:Binding Sites; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D018983:DNA Footprinting; D020407:Internet; D010802:Phylogeny; D012045:Regulatory Sequences, Nucleic Acid; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA