title: MatInspector and beyond: promoter analysis based on transcription factor binding sites.
abstract: BACKGROUND
  Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes.
  
  
  RESULTS
  We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).
authors.affiliation: Genomatix Software GmbH Landsberger Strasse. 6, 80339 München, Germany. cartharius@genomatix.de
authors.forename: K
authors.initials: K
authors.lastname: Cartharius
authors.forename: K
authors.initials: K
authors.lastname: Frech
authors.forename: K
authors.initials: K
authors.lastname: Grote
authors.forename: B
authors.initials: B
authors.lastname: Klocke
authors.forename: M
authors.initials: M
authors.lastname: Haltmeier
authors.forename: A
authors.initials: A
authors.lastname: Klingenhoff
authors.forename: M
authors.initials: M
authors.lastname: Frisch
authors.forename: M
authors.initials: M
authors.lastname: Bayerlein
authors.forename: T
authors.initials: T
authors.lastname: Werner
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D014157:Transcription Factors / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D014157:Transcription Factors