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Asymptotic Enumeration of RNA Structures with Pseudoknots


In this paper, we present the asymptotic enumeration of RNA structures with pseudoknots. We develop a general framework for the computation of exponential growth rate and the asymptotic expansion for the numbers of k-noncrossing RNA structures. Our results are based on the generating function for the number of k-noncrossing RNA pseudoknot structures, \({\mathsf{S}}_{k}(n)\) , derived in Bull. Math. Biol. (2008), where k−1 denotes the maximal size of sets of mutually intersecting bonds. We prove a functional equation for the generating function \(\sum_{n\ge 0}{\mathsf{S}}_{k}(n)z^{n}\) and obtain for k=2 and k=3, the analytic continuation and singular expansions, respectively. It is implicit in our results that for arbitrary k singular expansions exist and via transfer theorems of analytic combinatorics, we obtain asymptotic expression for the coefficients. We explicitly derive the asymptotic expressions for 2- and 3-noncrossing RNA structures. Our main result is the derivation of the formula \({\mathsf{S}}_{3}(n)\sim \frac{10.4724\cdot4!}{n(n-1)\cdots(n-4)}(\frac{5+\sqrt{21}}{2})^{n}\) .

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Correspondence to Christian M. Reidys.

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Jin, E.Y., Reidys, C.M. Asymptotic Enumeration of RNA Structures with Pseudoknots. Bull. Math. Biol. 70, 951–970 (2008).

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  • Asymptotic enumeration
  • RNA secondary structure
  • k-noncrossing RNA structure
  • Pseudoknot
  • Generating function
  • Transfer theorem
  • Hankel contour
  • Singular expansion