ArticleRNA (New York, N.Y.)2015
RNAMotifScanX: a graph alignment approach for RNA structural motif identification.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment.Nucleic acids research · 2026Article
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 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
- 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
- LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.Nucleic acids research · 2020Article
- De novo discovery of structural motifs in RNA 3D structures through clustering.Nucleic acids research · 2018Article
- CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures.Nucleic acids research · 2017Article
- STAR3D: a stack-based RNA 3D structural alignment tool.Nucleic acids research · 2015Article
Corrections and comments
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Authors and funding
2 authors.
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Abstract
RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture. These RNA structural motifs play important structural or functional roles and usually exhibit highly conserved 3D geometries and base-interaction patterns. Analysis of the RNA 3D structures and elucidation of their molecular functions heavily rely on efficient and accurate identification of these motifs. However, efficient RNA structural motif search tools are lacking due to the high complexity of these motifs. In this work, we present RNAMotifScanX, a motif search tool based on a base-interaction graph alignment algorithm. This novel algorithm enables automatic identification of both partially and fully matched motif instances. RNAMotifScanX considers noncanonical base-pairing interactions, base-stacking interactions, and sequence conservation of the motifs, which leads to significantly improved sensitivity and specificity as compared with other state-of-the-art search tools. RNAMotifScanX also adopts a carefully designed branch-and-bound technique, which enables ultra-fast search of large kink-turn motifs against a 23S rRNA. The software package RNAMotifScanX is implemented using GNU C++, and is freely available from http://genome.ucf.edu/RNAMotifScanX.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.