title: RNAlien - Unsupervised RNA family model construction.
abstract: Determining the function of a non-coding RNA requires costly and time-consuming wet-lab experiments. For this reason, computational methods which ascertain the homology of a sequence and thereby deduce functionality and family membership are often exploited. In this fashion, newly sequenced genomes can be annotated in a completely computational way. Covariance models are commonly used to assign novel RNA sequences to a known RNA family. However, to construct such models several examples of the family have to be already known. Moreover, model building is the work of experts who manually edit the necessary RNA alignment and consensus structure. Our method, RNAlien, starting from a single input sequence collects potential family member sequences by multiple iterations of homology search. RNA family models are fully automatically constructed for the found sequences. We have tested our method on a subset of the Rfam RNA family database. RNAlien models are a starting point to construct models of comparable sensitivity and specificity to manually curated ones from the Rfam database. RNAlien Tool and web server are available at http://rna.tbi.univie.ac.at/rnalien/.
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science University of Freiburg, Georges-Köhler-Allee, 79110 Freiburg, Germany egg@informatik.uni-freiburg.de.
authors.forename: Florian
authors.identifier: 0000-0001-9564-7525
authors.initials: F
authors.lastname: Eggenhofer
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, A-1090 Vienna, Austria.
authors.forename: Ivo L
authors.identifier: 0000-0001-7132-0800
authors.initials: IL
authors.lastname: Hofacker
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria Bioinformatics Group, Department of Computer Science, University of Leipzig, D-04107 Leipzig, Germany Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Höner Zu Siederdissen
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012689:Sequence Homology, Nucleic Acid; D013997:Time Factors
chemical_list: D012313:RNA