ArticleComputational and structural biotechnology journal2023
RNAsmc: A integrated tool for comparing RNA secondary structure and evaluating allosteric effects.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Divergent RNA structures support accurate splicing of the SF3B1-sensitivebioRxiv : the preprint server for biology · 2026Article
- Sequence optimization of a DNA aptamer inhibiting COVID-19 infection guided by analysis of secondary structure distribution.Computational and structural biotechnology journal · 2026Article
- Associating cancer-related RNA structure disrupting SNPs in LincRNAs to function.BMC genomics · 2025Article
- RNA-seq analyses reveal the relevance of RNAs involved in ribosomal complex to induce mammalian prion protein aggregation and phase separationRNA biology · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- StructRMDB: A database of RNA modification sites that affect RNA secondary structure.Computational and structural biotechnology journal · 2025Article
- Cross-population enhancement of PrediXcan predictions with a gnomAD-based east Asian reference framework.Briefings in bioinformatics · 2024Article
- scEGG: an exogenous gene-guided clustering method for single-cell transcriptomic data.Briefings in bioinformatics · 2024Article
- Probing RNA structural landscapes acrossFrontiers in microbiology · 2024Article
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Authors and funding
12 authors.
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Abstract
RNA structure plays a crucial role in gene regulation, in RNA stability and the essential biological processes. RNA secondary structure (RSS) motifs are the basic building blocks for investigating the biological mechanisms of structure. Here, we present a strategy for structural motif-based dynamic alignment, namely, RNA secondary-structural motif-comparing (RNAsmc), to identify structural motifs and quantitatively evaluate their underlying molecular functions. RNAsmc also has strong robustness to sequence length, folding protocol and RNA structural profile by chemical probing. Notably, it is also applicable to quantify structural variation in special RNA editing events (SNVs or SNPs, fragment insertion or deletion, etc.). The findings indicate that RNAsmc can uncover the heterogeneity of RNA secondary structure and score for similarities among components, which provides an impetus to cluster RNA families and evaluate allosteric effects. We find that RNAsmc exhibits remarkable detection efficiency for experimentally-derived RiboSNitches. Finally, the pipeline was assembled into an R software package to serve as an automated toolkit to explore, align, and cluster RSS. It is freely available for download at https://CRAN.R-project.org/package=RNAsmc.
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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.