Shapes of RNA pseudoknot structures

MaRDI QIDQ6214448zbMATH OpenFDO

Authors Christian M. Reidys, Rita R. Wang

Publication date 22 June 2009

Mathematics Subject Classification ID

Asymptotic enumeration (05A16)

Abstract: In this paper we study abstract shapes of $k$-noncrossing, $sigma$-canonical RNA pseudoknot structures. We consider ${sflv}_k^{sf1}$- and ${sflv}_k^{sf5}$-shapes, which represent a generalization of the abstract $p{i}^{\prime }$- and $pi$-shapes of RNA secondary structures introduced by citet{Giegerich:04ashape}. Using a novel approach we compute the generating functions of ${sflv}_k^{sf1}$- and ${sflv}_k^{sf5}$-shapes as well as the generating functions of all ${sflv}_k^{sf1}$- and ${sflv}_k^{sf5}$-shapes induced by all $k$-noncrossing, $sigma$-canonical RNA structures for fixed $n$. By means of singularity analysis of the generating functions, we derive explicit asymptotic expressions.

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