ArticleRNA (New York, N.Y.)2023
bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.
Article in RNA (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Tree_RNA-Align: RNA Secondary Structure Clustering and Classification Based on Tree-Structure Alignment.International journal of molecular sciences · 2026Article
- Sequence optimization of a DNA aptamer inhibiting COVID-19 infection guided by analysis of secondary structure distribution.Computational and structural biotechnology journal · 2026Article
- Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.Nucleic acids research · 2025Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.bioRxiv : the preprint server for biology · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Short tandem repeat variants are possibly associated with RNA secondary structure and gene expression.PloS one · 2025Article
- Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts.Biology methods & protocols · 2025Article
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2 authors.
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Abstract
Ribonucleic acid (RNA) is a polymeric molecule that is fundamental to biological processes, with structure being more highly conserved than primary sequence and often key to its function. Advances in RNA structure characterization have resulted in an increase in the number of accurate secondary structures. The task of uncovering common RNA structural motifs with a collective function through structural comparison, providing a level of similarity, remains challenging and could be used to improve RNA secondary structure databases and discover new RNA families. In this work, we present a novel secondary structure alignment method, bpRNA-align. bpRNA-align is a customized global structural alignment method, utilizing an inverted (gap extend costs more than gap open) and context-specific affine gap penalty along with a structural, feature-specific substitution matrix to provide similarity scores. We evaluate our similarity scores in comparison to other methods, using affinity propagation clustering, applied to a benchmarking data set of known structure types. bpRNA-align shows improvement in clustering performance over a broad range of structure types.
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