title: MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data.
abstract: CONCLUSIONS
  Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.
  
  
  BACKGROUND
  MOTIFATOR is freely available at http://www.motifator.nl.
authors.affiliation: Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV Groningen, The Netherlands.
authors.forename: Evert-Jan
authors.initials: EJ
authors.lastname: Blom
authors.forename: Jos B T M
authors.initials: JB
authors.lastname: Roerdink
authors.forename: Oscar P
authors.initials: OP
authors.lastname: Kuipers
authors.forename: Sacha A F T
authors.initials: SA
authors.lastname: van Hijum
mesh_terms: D017124:Conserved Sequence; D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011387:Prokaryotic Cells; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D012984:Software