title: Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
abstract: Recent progress in predicting RNA structure is moving towards filling the 'gap' in 2D RNA structure prediction where, for example, predicted internal loops often form non-canonical base pairs. This is increasingly recognized with the steady increase of known RNA 3D modules. There is a general interest in matching structural modules known from one molecule to other molecules for which the 3D structure is not known yet. We have created a pipeline, metaRNAmodules, which completely automates extracting putative modules from the FR3D database and mapping of such modules to Rfam alignments to obtain comparative evidence. Subsequently, the modules, initially represented by a graph, are turned into models for the RMDetect program, which allows to test their discriminative power using real and randomized Rfam alignments. An initial extraction of 22 495 3D modules in all PDB files results in 977 internal loop and 17 hairpin modules with clear discriminatory power. Many of these modules describe only minor variants of each other. Indeed, mapping of the modules onto Rfam families results in 35 unique locations in 11 different families. The metaRNAmodules pipeline source for the internal loop modules is available at http://rth.dk/resources/mrm.
authors.affiliation: Center for non-coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg, Denmark, Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria and Research Group Bioinformatics and Computational Biology, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria.
authors.forename: Corinna
authors.initials: C
authors.lastname: Theis
authors.forename: Christian
authors.initials: C
authors.lastname: Höner Zu Siederdissen
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
mesh_terms: D001483:Base Sequence; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D012984:Software
chemical_list: D012313:RNA