Shapes of RNA pseudoknot structures

Details Shapes of RNA pseudoknot structures Shapes of RNA pseudoknot structures

2009-06-22

arxiv.org/abs/0906.3999v2

Mathematics

Combinatorics

24 pages, 7 figures,

Scientific paper

In this paper we study abstract shapes of $k$-noncrossing, $\sigma$-canonical RNA pseudoknot structures. We consider ${\sf lv}_k^{\sf 1}$- and ${\sf lv}_k^{\sf 5}$-shapes, which represent a generalization of the abstract $\pi'$- and $\pi$-shapes of RNA secondary structures introduced by \citet{Giegerich:04ashape}. Using a novel approach we compute the generating functions of ${\sf lv}_k^{\sf 1}$- and ${\sf lv}_k^{\sf 5}$-shapes as well as the generating functions of all ${\sf lv}_k^{\sf 1}$- and ${\sf lv}_k^{\sf 5}$-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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