title: ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species.
abstract: Transcription factors (TFs) are key components in signaling pathways, and the presence of their binding sites in the promoter regions of DNA is essential for their regulation of the expression of the corresponding genes. Orthologous promoter sequences are commonly used to increase the specificity with which potentially functional transcription factor binding sites (TFBSs) are recognized and to detect possibly important similarities or differences between the different species. The ConTra (conserved TFBSs) web server provides the biologist at the bench with a user-friendly tool to interactively visualize TFBSs predicted using either TransFac (1) or JASPAR (2) position weight matrix libraries, on a promoter alignment of choice. The visualization can be preceded by a simple scoring analysis to explore which TFs are the most likely to bind to the promoter of interest. The ConTra web server is available at http://bioit.dmbr.ugent.be/ConTra/index.php.
authors.affiliation: Bioinformatics Core Facility, VIB, Department of Molecular Biology, Ghent University and Department for Molecular Biomedical Research, VIB, B-9052 Ghent, Belgium.
authors.forename: Bart
authors.initials: B
authors.lastname: Hooghe
authors.forename: Paco
authors.initials: P
authors.lastname: Hulpiau
authors.forename: Frans
authors.initials: F
authors.lastname: van Roy
authors.forename: Pieter
authors.initials: P
authors.lastname: De Bleser
mesh_terms: D000818:Animals; D001665:Binding Sites; D003196:Computer Graphics; D006801:Humans; D020407:Internet; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors