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

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

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 l...

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Bibliographic Details
Published in:Nucleic acids research Vol. 39; no. 8; pp. 3418 - 3426
Main Authors: Pánek, Josef, Krásny, Libor, Bobek, Jan, Jezková, Edita, Korelusová, Jana, Vohradsky, Jirí
Format: Journal Article
Language:English
Published: England Oxford University Press 01-04-2011
Subjects:
Bacteria
Base Sequence
Computer applications
Conservation
Evolution
Evolutionary conservation
Genomes
Homology
Molecular Sequence Data
Mycobacterium - genetics
non-coding RNA
Nucleic Acid Conformation
Prokaryotes
RNA
RNA, Bacterial - chemistry
RNA, Untranslated - chemistry
Sequence Homology, Nucleic Acid
Streptomyces - genetics
Synteny
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Summary: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.
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ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkq1186