title: RILogo: visualizing RNA-RNA interactions.
abstract: CONCLUSIONS
  With the increasing amount of newly discovered non-coding RNAs, the interactions between RNA molecules become an increasingly important aspect for characterizing their functionality. Many computational tools have been developed to predict the formation of duplexes between two RNAs, either based on single sequences or alignments of homologous sequences. Here, we present RILogo, a program to visualize inter- and intramolecular base pairing between two RNA molecules. The input for RILogo is a pair of structure-annotated sequences or alignments. In the latter case, RILogo displays the alignments in the form of sequence logos, including the mutual information of base paired columns. We also introduce two novel mutual information based measures that weigh the covariance information by the evolutionary distances of the aligned sequences. We show that the new measures have an increased accuracy compared with previous mutual information measures.
  
  
  METHODS
  RILogo is freely available as a stand-alone program and is accessible via a web server at http://rth.dk/resources/rilogo.
  
  
  BACKGROUND
  pmenzel@gmail.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen DK-2200, Denmark. pmenzel@gmail.com
authors: Peter
authors: P
authors: Menzel
authors: Stefan E
authors: SE
authors: Seemann
authors: Jan
authors: J
authors: Gorodkin
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D020407:Internet; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D022661:RNA, Untranslated