Combinatorics of RNA-RNA interaction
No Thumbnail Available
Date
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
Abstract
Description
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.
27 pages, 12 figures
27 pages, 12 figures
Keywords
Combinatorics, Soft Condensed Matter, Biological Physics, Biomolecules, 05A16 92E10