title: PromAn: an integrated knowledge-based web server dedicated to promoter analysis.
abstract: PromAn is a modular web-based tool dedicated to promoter analysis that integrates distinct complementary databases, methods and programs. PromAn provides automatic analysis of a genomic region with minimal prior knowledge of the genomic sequence. Prediction programs and experimental databases are combined to locate the transcription start site (TSS) and the promoter region within a large genomic input sequence. Transcription factor binding sites (TFBSs) can be predicted using several public databases and user-defined motifs. Also, a phylogenetic footprinting strategy, combining multiple alignment of large genomic sequences and assignment of various scores reflecting the evolutionary selection pressure, allows for evaluation and ranking of TFBS predictions. PromAn results can be displayed in an interactive graphical user interface, PromAnGUI. It integrates all of this information to highlight active promoter regions, to identify among the huge number of TFBS predictions those which are the most likely to be potentially functional and to facilitate user refined analysis. Such an integrative approach is essential in the face of a growing number of tools dedicated to promoter analysis in order to propose hypotheses to direct further experimental validations. PromAn is publicly available at http://bips.u-strasbg.fr/PromAn.
authors.affiliation: Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, BP 163, 67404 Illkirch Cedex, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Lardenois
authors.forename: Frédéric
authors.initials: F
authors.lastname: Chalmel
authors.forename: Laurent
authors.initials: L
authors.lastname: Bianchetti
authors.forename: José-Alain
authors.initials: JA
authors.lastname: Sahel
authors.forename: Thierry
authors.initials: T
authors.lastname: Léveillard
authors.forename: Olivier
authors.initials: O
authors.lastname: Poch
mesh_terms: D001665:Binding Sites; D030541:Databases, Genetic; D023281:Genomics / Q000379:methods*; D020407:Internet; D011401:Promoter Regions, Genetic; D016415:Sequence Alignment; D012984:Software; D018511:Systems Integration; D014157:Transcription Factors / Q000378:metabolism*; D024363:Transcription Initiation Site; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors