title: The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures.
abstract: Non-coding RNAs (ncRNAs) are regulatory molecules encoded in the intergenic or intragenic regions of the genome. In prokaryotes, biocomputational identification of homologs of known ncRNAs in other species often fails due to weakly evolutionarily conserved sequences, structures, synteny and genome localization, except in the case of evolutionarily closely related species. To eliminate results from weak conservation, we focused on RNA structure, which is the most conserved ncRNA property. Analysis of the structure of one of the few well-studied bacterial ncRNAs, 6S RNA, demonstrated that unlike optimal and consensus structures, suboptimal structures are capable of capturing RNA homology even in divergent bacterial species. A computational procedure for the identification of homologous ncRNAs using suboptimal structures was created. The suggested procedure was applied to strongly divergent bacterial species and was capable of identifying homologous ncRNAs.
authors.affiliation: Laboratory of Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1073, 14220 Prague, Czech Republic. panek@biomed.cas.cz
authors.forename: Josef
authors.initials: J
authors.lastname: Pánek
authors.forename: Libor
authors.initials: L
authors.lastname: Krásny
authors.forename: Jan
authors.initials: J
authors.lastname: Bobek
authors.forename: Edita
authors.initials: E
authors.lastname: Jezková
authors.forename: Jana
authors.initials: J
authors.lastname: Korelusová
authors.forename: Jirí
authors.initials: J
authors.lastname: Vohradsky
mesh_terms: D001483:Base Sequence; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000235:genetics; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000737:chemistry*; D022661:RNA, Untranslated / Q000737:chemistry*; D012689:Sequence Homology, Nucleic Acid; D013302:Streptomyces / Q000235:genetics
chemical_list: C411065:6S RNA; D012329:RNA, Bacterial; D022661:RNA, Untranslated