title: DiffLogo: a comparative visualization of sequence motifs.
abstract: BACKGROUND
  For three decades, sequence logos are the de facto standard for the visualization of sequence motifs in biology and bioinformatics. Reasons for this success story are their simplicity and clarity. The number of inferred and published motifs grows with the number of data sets and motif extraction algorithms. Hence, it becomes more and more important to perceive differences between motifs. However, motif differences are hard to detect from individual sequence logos in case of multiple motifs for one transcription factor, highly similar binding motifs of different transcription factors, or multiple motifs for one protein domain.
  
  
  RESULTS
  Here, we present DiffLogo, a freely available, extensible, and user-friendly R package for visualizing motif differences. DiffLogo is capable of showing differences between DNA motifs as well as protein motifs in a pair-wise manner resulting in publication-ready figures. In case of more than two motifs, DiffLogo is capable of visualizing pair-wise differences in a tabular form. Here, the motifs are ordered by similarity, and the difference logos are colored for clarity. We demonstrate the benefit of DiffLogo on CTCF motifs from different human cell lines, on E-box motifs of three basic helix-loop-helix transcription factors as examples for comparison of DNA motifs, and on F-box domains from three different families as example for comparison of protein motifs.
  
  
  CONCLUSIONS
  DiffLogo provides an intuitive visualization of motif differences. It enables the illustration and investigation of differences between highly similar motifs such as binding patterns of transcription factors for different cell types, treatments, and algorithmic approaches.
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany. martin.nettling@informatik.uni-halle.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Nettling
authors.affiliation: Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany. hendrik.treutler@ipb-halle.de.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Treutler
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany. jan.grau@informatik.uni-halle.de.
authors.forename: Jan
authors.initials: J
authors.lastname: Grau
authors.affiliation: Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Quedlinburg, Germany. jens.keilwagen@jki.bund.de.
authors.forename: Jens
authors.initials: J
authors.lastname: Keilwagen
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany. stefan.posch@informatik.uni-halle.de.
authors.forename: Stefan
authors.initials: S
authors.lastname: Posch
authors.affiliation: Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany. ivo.grosse@informatik.uni-halle.de.|German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. ivo.grosse@informatik.uni-halle.de.
authors.forename: Ivo
authors.initials: I
authors.lastname: Grosse
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs / Q000235:genetics*; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics*; D000076246:CCCTC-Binding Factor; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D006801:Humans; D059372:Nucleotide Motifs / Q000235:genetics*; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D014407:Tumor Cells, Cultured
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D000076246:CCCTC-Binding Factor; D012097:Repressor Proteins; C000619697:CTCF protein, human