ArticleNucleic acids research2010
RNAMotifScan: automatic identification of RNA structural motifs using secondary structural alignment.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- 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
- RNALigands: a database and web server for RNA-ligand interactions.RNA (New York, N.Y.) · 2022Article
- On the predictibility of A-minor motifs from their local contexts.RNA biology · 2022Article
- Graph Theoretical Methods and Workflows for Searching and Annotation of RNA Tertiary Base Motifs and Substructures.International journal of molecular sciences · 2021Review
- RNAMotifContrast: a method to discover and visualize RNA structural motif subfamilies.Nucleic acids research · 2021Article
- Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.PLoS computational biology · 2021Article
- DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data.Frontiers in genetics · 2021Article
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
- A unified dinucleotide alphabet describing both RNA and DNA structures.Nucleic acids research · 2020Article
- Automated, customizable and efficient identification of 3D base pair modules with BayesPairing.Nucleic acids research · 2019Article
- De novo discovery of structural motifs in RNA 3D structures through clustering.Nucleic acids research · 2018Article
- Mining for recurrent long-range interactions in RNA structures reveals embedded hierarchies in network families.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Long Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function.Circulation research · 2018Review
- CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.Nucleic acids research · 2017Article
- RNAMotifScanX: a graph alignment approach for RNA structural motif identification.RNA (New York, N.Y.) · 2015Article
- The role of nucleobase interactions in RNA structure and dynamics.Nucleic acids research · 2014Article
- RASS: a web server for RNA alignment in the joint sequence-structure space.Nucleic acids research · 2014Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have shown that RNA structural motifs play essential roles in RNA folding and interaction with other molecules. Computational identification and analysis of RNA structural motifs remains a challenging task. Existing motif identification methods based on 3D structure may not properly compare motifs with high structural variations. Other structural motif identification methods consider only nested canonical base-pairing structures and cannot be used to identify complex RNA structural motifs that often consist of various non-canonical base pairs due to uncommon hydrogen bond interactions. In this article, we present a novel RNA structural alignment method for RNA structural motif identification, RNAMotifScan, which takes into consideration the isosteric (both canonical and non-canonical) base pairs and multi-pairings in RNA structural motifs. The utility and accuracy of RNAMotifScan is demonstrated by searching for kink-turn, C-loop, sarcin-ricin, reverse kink-turn and E-loop motifs against a 23S rRNA (PDBid: 1S72), which is well characterized for the occurrences of these motifs. Finally, we search these motifs against the RNA structures in the entire Protein Data Bank and the abundances of them are estimated. RNAMotifScan is freely available at our supplementary website (http://genome.ucf.edu/RNAMotifScan).
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