ArticleJournal of mathematical biology2014
Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding.
Article in Journal of mathematical biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 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
- Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.Journal of the Royal Society, Interface · 2017Article
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2 authors.
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Abstract
We analyze the distribution of RNA secondary structures given by the Knudsen-Hein stochastic context-free grammar used in the prediction program Pfold. Our main theorem gives relations between the expected number of these motifs--independent of the grammar probabilities. These relations are a consequence of proving that the distribution of base pairs, of helices, and of different types of loops is asymptotically Gaussian in this model of RNA folding. Proof techniques use singularity analysis of probability generating functions. We also demonstrate that these asymptotic results capture well the expected number of RNA base pairs in native ribosomal structures, and certain other aspects of their predicted secondary structures. In particular, we find that the predicted structures largely satisfy the expected relations, although the native structures do not.
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