ArticleNucleic acids research2011
The suboptimal structures find the optimal RNAs: homology search for bacterial non-coding RNAs using suboptimal RNA structures.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Expanding the CarD interaction network: CrsL is a novel transcription regulator in actinobacteria.Nucleic acids research · 2025Article
- ECSFinder: optimized prediction of evolutionarily conserved RNA secondary structures from genome sequences.Nucleic acids research · 2025Article
- MoaB2, a newly identified transcription factor, binds to σJournal of bacteriology · 2024Article
- RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria.Nucleic acids research · 2024Article
- Dynamic Transcriptional Landscape ofInternational journal of molecular sciences · 2023Article
- Ms1 RNA Interacts With the RNA Polymerase Core inFrontiers in microbiology · 2022Article
- 6S-Like scr3559 RNA Affects Development and Antibiotic Production inMicroorganisms · 2021Article
- Diversity and prevalence of ANTAR RNAs across actinobacteria.BMC microbiology · 2021Article
- rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output.Frontiers in genetics · 2020Article
- On a stake-out:Non-coding RNA research · 2019Review
- RCPred: RNA complex prediction as a constrained maximum weight clique problem.BMC bioinformatics · 2019Article
- rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots.Database : the journal of biological databases and curation · 2019Article
- aliFreeFold: an alignment-free approach to predict secondary structure from homologous RNA sequences.Bioinformatics (Oxford, England) · 2018Article
- 6S RNA, a Global Regulator of Transcription.Microbiology spectrum · 2018Review
- Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria.Nucleic acids research · 2014Article
- Dissemination of 6S RNA among bacteria.RNA biology · 2014Article
- Review
- Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis.PLoS pathogens · 2011Article
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6 authors.
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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.
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