ArticleInternational journal of molecular sciences2026
Tree_RNA-Align: RNA Secondary Structure Clustering and Classification Based on Tree-Structure Alignment.
Article in International journal of molecular sciences, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Clustering and classification of RNA secondary structures are central to understanding RNA function. However, widely used alignment methods, such as LocARNA and bpRNA-align, are not explicitly designed to exploit the hierarchical relationships among RNA structural elements, limiting their applicability to complex, multi-branched structures. In this study, we introduce Tree_RNA-Align, a novel method for RNA secondary structure clustering and classification based on a tree-structure alignment algorithm. The method transforms dot-bracket structures into tree representations, in which multibranch loops and stems serve as nodes, thereby preserving the hierarchical relationships among structural elements. It integrates a bottom-up hierarchical comparison for clustering with a top-down comparison for classification and prediction. Notably, classification experiments on five RNA families (16S rRNA, group_I_intron, RNase P, SRP, and tmRNA) achieved a micro-averaged
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