Combinatorics of RNA-RNA interaction

Details Combinatorics of RNA-RNA interaction Combinatorics of RNA-RNA interaction

2010-06-15

arxiv.org/abs/1006.2924v1

Mathematics

Combinatorics

27 pages, 12 figures

Scientific paper

RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called ``zig-zag'' configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number of joint structures.

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