RNA pseudoknot structures with arc-length 3 and stack-length

DOI10.1016/J.DAM.2009.08.004zbMATH Open1197.92016arXiv0708.3134OpenAlexW2038697696MaRDI QIDQ968109FDOQ968109

Authors: Christian M. Reidys, Emma Yu Jin 

Publication date: 5 May 2010

Published in: Discrete Applied Mathematics (Search for Journal in Brave)

Abstract: In this paper we study $k$-noncrossing RNA structures with arc-length $ge3$, i.e. RNA molecules in which for any $i$, the nucleotides labeled $i$ and $i+j$ ($j=1,2$) cannot form a bond and in which there are at most $k-1$ mutually crossing arcs. Let ${sfS}_{k,3}(n)$ denote their number. Based on a novel functional equation for the generating function $su{m}_{nge0}{sfS}_{k,3}(n)z^n$, we derive for arbitrary $kge3$ exponential growth factors and for $k=3$ the subexponential factor. Our main result is the derivation of the formula ${sfS}_{3,3}(n)simfrac6.11170cdot4!n(n-1)\mathrm{...}(n-4)4.54920^n$.

Full work available at URL: https://arxiv.org/abs/0708.3134

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zbMATH Keywords

generating functionenumerationRNA secondary structurepseudoknot

Mathematics Subject Classification ID

Applications of graph theory (05C90) Biochemistry, molecular biology (92C40)

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Cited In (16)

• On the decomposition of \(k\)-noncrossing RNA structures
• An integer linear programming problem for RNA structures
• Statistics of canonical RNA pseudoknot structures
• Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
• RNA structures with pseudo-knots: graph-theoretical, combinatorial, and statistical properties
• Asymptotic enumeration of RNA structures with pseudoknots
• Stacks in canonical RNA pseudoknot structures
• A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes
• Properties of RNA secondary structure matching models
• Enumerating RNA structures, including pseudoknots of any topology
• Irreducibility in RNA structures
• On the page number of RNA secondary structures with pseudoknots
• Random \(k\)-noncrossing RNA structures
• Central and local limit theorems for RNA structures
• Counting RNA pseudoknotted structures (extended abstract)
• The block spectrum of RNA pseudoknot structures

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