The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAsusing suboptimal RNA structures

0354394 - MBÚ 2011 RIV GB eng J - Journal Article
Pánek, Josef - Krásný, Libor - Bobek, Jan - Ježková, E. - Korelusová, Jana - Vohradský, Jiří
The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAsusing suboptimal RNA structures.
Nucleic Acids Research. -, - (2010), s. 1-9. ISSN 0305-1048. E-ISSN 1362-4962
R&D Projects: GA MŠMT 2B06065; GA ČR GA303/09/0475; GA ČR GA310/07/1009
Institutional research plan: CEZ:AV0Z50200510
Keywords : ncRNAs * RNA structures
Subject RIV: EE - Microbiology, Virology
Impact factor: 7.836, year: 2010

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 wellstudied 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
Permanent Link: http://hdl.handle.net/11104/0193405