ArticleNucleic acids research2012
Clustering RNA structural motifs in ribosomal RNAs using secondary structural alignment.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- All-at-once RNA folding with 3D motif prediction framed by evolutionary information.Nature methods · 2025Article
- GINClus: RNA structural motif clustering using graph isomorphism network.NAR genomics and bioinformatics · 2025Article
- RNAMotifProfile: a graph-based approach to build RNA structural motif profiles.NAR genomics and bioinformatics · 2024Article
- RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families.Bioinformatics (Oxford, England) · 2023Article
- CircularSTAR3D: a stack-based RNA 3D structural alignment tool for circular matching.Nucleic acids research · 2023Article
- RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies.Nucleic acids research · 2021Article
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
- Identification and Characterization of New RNA Tetraloop Sequence Families.Biochemistry · 2019Article
- Article
- De novo discovery of structural motifs in RNA 3D structures through clustering.Nucleic acids research · 2018Article
- Mapping the Universe of RNA Tetraloop Folds.Biophysical journal · 2017Article
- Long noncoding RNAs in the progression, metastasis, and prognosis of osteosarcoma.Cell death & disease · 2016Review
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
- RNAMotifScanX: a graph alignment approach for RNA structural motif identification.RNA (New York, N.Y.) · 2015Article
- Annotating RNA motifs in sequences and alignments.Nucleic acids research · 2015Article
- Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.Nucleic acids research · 2014Article
- Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.Nucleic acids research · 2013Article
- Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.The journal of physical chemistry. B · 2013Article
- Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas.RNA (New York, N.Y.) · 2013Article
- An innate twist between Crick's wobble and Watson-Crick base pairs.RNA (New York, N.Y.) · 2013Review
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA structural motifs are the building blocks of the complex RNA architecture. Identification of non-coding RNA structural motifs is a critical step towards understanding of their structures and functionalities. In this article, we present a clustering approach for de novo RNA structural motif identification. We applied our approach on a data set containing 5S, 16S and 23S rRNAs and rediscovered many known motifs including GNRA tetraloop, kink-turn, C-loop, sarcin-ricin, reverse kink-turn, hook-turn, E-loop and tandem-sheared motifs, with higher accuracy than the state-of-the-art clustering method. We also identified a number of potential novel instances of GNRA tetraloop, kink-turn, sarcin-ricin and tandem-sheared motifs. More importantly, several novel structural motif families have been revealed by our clustering analysis. We identified a highly asymmetric bulge loop motif that resembles the rope sling. We also found an internal loop motif that can significantly increase the twist of the helix. Finally, we discovered a subfamily of hexaloop motif, which has significantly different geometry comparing to the currently known hexaloop motif. Our discoveries presented in this article have largely increased current knowledge of RNA structural motifs.
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