Canonical RNA pseudoknot structures

MaRDI QIDQ6209921zbMATH OpenFDO

Authors Gang Ma, Christian M. Reidys

Publication date 14 June 2008

Mathematics Subject Classification ID

Rational and ruled surfaces (14J26) Vector bundles on surfaces and higher-dimensional varieties, and their moduli (14J60)

Abstract: In this paper we study $k$-noncrossing, canonical RNA pseudoknot structures with minimum arc-length $ge4$. Let ${sfT}_{k,sigma}^{[4]}(n)$ denote the number of these structures. We derive exact enumeration results by computing the generating function $$ and derive the asymptotic formulas ${sfT}_{k,3}^{[4]}(n{)}^{}sim{c}_k{n}^{-(k-1{)}^2-frack-12}(gamm{a}_{k,3}^{[4]}{)}^{-n}$ for $k=3,\mathrm{...},9$. In particular we have for $k=3$, ${sfT}_{3,3}^{[4]}(n{)}^{}sim{c}_3{n}^{-5}2.0348^n$. Our results prove that the set of biophysically relevant RNA pseudoknot structures is surprisingly small and suggest a new structure class as target for prediction algorithms.

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