ArticleBMC genomics2014
Efficient calculation of exact probability distributions of integer features on RNA secondary structures.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Making Ends Meet or Just Meeting at the Ends? Assessing End-to-End Distance in Folded RNA Sequences and Other Branched Structures.Bulletin of mathematical biology · 2026Article
- Investigating the Prevalence of RNA-Binding Metabolic Enzymes inInternational journal of molecular sciences · 2023Article
- Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp.BMC bioinformatics · 2020Article
- Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.BMC bioinformatics · 2018Article
- Rtools: a web server for various secondary structural analyses on single RNA sequences.Nucleic acids research · 2016Article
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Authors and funding
3 authors.
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Abstract
backgroundAlthough the needs for analyses of secondary structures of RNAs are increasing, prediction of the secondary structures of RNAs are not always reliable. Because an RNA may have a complicated energy landscape, comprehensive representations of the whole ensemble of the secondary structures, such as the probability distributions of various features of RNA secondary structures are required.
resultsA general method to efficiently compute the distribution of any integer scalar/vector function on the secondary structure is proposed. We also show two concrete algorithms, for Hamming distance from a reference structure and for 5'-3' distance, which can be constructed by following our general method. These practical applications of this method show the effectiveness of the proposed method.
conclusionsThe proposed method provides a clear and comprehensive procedure to construct algorithms for distributions of various integer features. In addition, distributions of integer vectors, that is a combination of different integer scores, can be also described by applying our 2D expanding technique.
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