title: Search for 5'-leader regulatory RNA structures based on gene annotation aided by the RiboGap database.
abstract: The discovery of noncoding RNAs (ncRNAs) and their importance for gene regulation led us to develop bioinformatics tools to pursue the discovery of novel ncRNAs. Finding ncRNAs de novo is challenging, first due to the difficulty of retrieving large numbers of sequences for given gene activities, and second due to exponential demands on calculation needed for comparative genomics on a large scale. Recently, several tools for the prediction of conserved RNA secondary structure were developed, but many of them are not designed to uncover new ncRNAs, or are too slow for conducting analyses on a large scale. Here we present various approaches using the database RiboGap as a primary tool for finding known ncRNAs and for uncovering simple sequence motifs with regulatory roles. This database also can be used to easily extract intergenic sequences of eubacteria and archaea to find conserved RNA structures upstream of given genes. We also show how to extend analysis further to choose the best candidate ncRNAs for experimental validation.
authors.affiliation: INRS - Institut Armand-Frappier, 531 boul des Prairies, Laval (Québec) H7V1B7, Canada.
authors.forename: Mohammad Reza
authors.initials: MR
authors.lastname: Naghdi
authors.affiliation: INRS - Institut Armand-Frappier, 531 boul des Prairies, Laval (Québec) H7V1B7, Canada.
authors.forename: Katia
authors.initials: K
authors.lastname: Smail
authors.affiliation: Department of Molecular, Cellular and Developmental Biology and the Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, United States.
authors.forename: Joy X
authors.initials: JX
authors.lastname: Wang
authors.affiliation: INRS - Institut Armand-Frappier, 531 boul des Prairies, Laval (Québec) H7V1B7, Canada.
authors.forename: Fallou
authors.initials: F
authors.lastname: Wade
authors.affiliation: Department of Molecular, Cellular and Developmental Biology and the Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, United States.
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
authors.affiliation: INRS - Institut Armand-Frappier, 531 boul des Prairies, Laval (Québec) H7V1B7, Canada. Electronic address: jonathan.perreault@iaf.inrs.ca.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Perreault
mesh_terms: D000465:Algorithms; D000818:Animals; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D006801:Humans; D058977:Molecular Sequence Annotation; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry / Q000145:classification / Q000235:genetics*; D058928:Riboswitch; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D022661:RNA, Untranslated; D058928:Riboswitch
keywords: Bioinformatics; CsrA; GraphClust; Infernal; Methyltransferase; RNA secondary structure; Rfam; Riboswitch; RsmA; TRAP; ncRNA