title: InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites.
abstract: Recent studies have shown that the traditional position weight matrix model is often insufficient for modeling transcription factor binding sites, as intra-motif dependencies play a significant role for an accurate description of binding motifs. Here, we present the Java application InMoDe, a collection of tools for learning, leveraging and visualizing such dependencies of putative higher order. The distinguishing feature of InMoDe is a robust model selection from a class of parsimonious models, taking into account dependencies only if justified by the data while choosing for simplicity otherwise.
  
  
  
  InMoDe is implemented in Java and is available as command line application, as application with a graphical user-interface, and as an integration into Galaxy on the project website at http://www.jstacs.de/index.php/InMoDe .
  
  
  
  ralf.eggeling@cs.helsinki.fi.
authors.affiliation: Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Helsinki, Finland.
authors.forename: Ralf
authors.initials: R
authors.lastname: Eggeling
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.|German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
authors.forename: Ivo
authors.initials: I
authors.lastname: Grosse
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Grau
mesh_terms: D000818:Animals; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D006801:Humans; D000069550:Machine Learning; D011401:Promoter Regions, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D014157:Transcription Factors; D004247:DNA