ArticleNucleic acids research2014
A novel approach to represent and compare RNA secondary structures.
Article in Nucleic acids research, 2014. 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.
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- miRVim: Three-dimensional miRNA Structure Database.MicroRNA (Shariqah, United Arab Emirates) · 2025Article
- Simulated Annealing for RNA Design with SIMARD.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Identification of potential riboswitch elements in Homo sapiens mRNA 5'UTR sequences using positive-unlabeled machine learning.PloS one · 2025Article
- Human lncRNAs harbor conserved modules embedded in different sequence contexts.Non-coding RNA research · 2024Article
- Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution.Nature communications · 2024Article
- bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.RNA (New York, N.Y.) · 2023Article
- RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects.Computational and structural biotechnology journal · 2023Article
- PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins.Nucleic acids research · 2022Article
- RNALigands: a database and web server for RNA-ligand interactions.RNA (New York, N.Y.) · 2022Article
- Comparative genomics in the search for conserved long noncoding RNAs.Essays in biochemistry · 2021Article
- BRIO: a web server for RNA sequence and structure motif scan.Nucleic acids research · 2021Article
- Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments.NAR genomics and bioinformatics · 2021Article
- Motif Discovery from CLIP Experiments.Methods in molecular biology (Clifton, N.J.) · 2021Article
- LncLocation: Efficient Subcellular Location Prediction of Long Non-Coding RNA-Based Multi-Source Heterogeneous Feature Fusion.International journal of molecular sciences · 2020Article
- The RNA secondary structural variation in the cyclization elements of the dengue genome and the possible implications in pathogenicity.Virusdisease · 2020Article
- PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.Communications biology · 2020Article
- The computational approaches of lncRNA identification based on coding potential:Computational and structural biotechnology journal · 2020Review
- LncFinder: an integrated platform for long non-coding RNA identification utilizing sequence intrinsic composition, structural information and physicochemical property.Briefings in bioinformatics · 2019Review
- Discovering sequence and structure landscapes in RNA interaction motifs.Nucleic acids research · 2019Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Structural information is crucial in ribonucleic acid (RNA) analysis and functional annotation; nevertheless, how to include such structural data is still a debated problem. Dot-bracket notation is the most common and simple representation for RNA secondary structures but its simplicity leads also to ambiguity requiring further processing steps to dissolve. Here we present BEAR (Brand nEw Alphabet for RNA), a new context-aware structural encoding represented by a string of characters. Each character in BEAR encodes for a specific secondary structure element (loop, stem, bulge and internal loop) with specific length. Furthermore, exploiting this informative and yet simple encoding in multiple alignments of related RNAs, we captured how much structural variation is tolerated in RNA families and convert it into transition rates among secondary structure elements. This allowed us to compute a substitution matrix for secondary structure elements called MBR (Matrix of BEAR-encoded RNA secondary structures), of which we tested the ability in aligning RNA secondary structures. We propose BEAR and the MBR as powerful resources for the RNA secondary structure analysis, comparison and classification, motif finding and phylogeny.
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