title: ConTra v2: a tool to identify transcription factor binding sites across species, update 2011.
abstract: Transcription factors are important gene regulators with distinctive roles in development, cell signaling and cell cycling, and they have been associated with many diseases. The ConTra v2 web server allows easy visualization and exploration of predicted transcription factor binding sites in any genomic region surrounding coding or non-coding genes. In this new version, users can choose from nine reference organisms ranging from human to yeast. ConTra v2 can analyze promoter regions, 5'-UTRs, 3'-UTRs and introns or any other genomic region of interest. Hundreds of position weight matrices are available to choose from, but the user can also upload any other matrices for detecting specific binding sites. A typical analysis is run in four simple steps of choosing the gene, the transcript, the region of interest and then selecting one or more transcription factor binding sites. The ConTra v2 web server is freely available at http://bioit.dmbr.ugent.be/contrav2/index.php.
authors.affiliation: Department for Molecular Biomedical Research, VIB, Ghent University, Ghent, Belgium. stefanb@dmbr.vib-ugent.be
authors.forename: Stefan
authors.initials: S
authors.lastname: Broos
authors.forename: Paco
authors.initials: P
authors.lastname: Hulpiau
authors.forename: Jeroen
authors.initials: J
authors.lastname: Galle
authors.forename: Bart
authors.initials: B
authors.lastname: Hooghe
authors.forename: Frans
authors.initials: F
authors.lastname: Van Roy
authors.forename: Pieter
authors.initials: P
authors.lastname: De Bleser
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D006801:Humans; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D050436:Regulatory Elements, Transcriptional; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors