Journal
JOURNAL OF MATHEMATICAL BIOLOGY
Volume 64, Issue 3, Pages 529-556Publisher
SPRINGER
DOI: 10.1007/s00285-011-0423-7
Keywords
RNA-RNA interaction; Joint structure; Shape; Symbolic enumeration; Singularity analysis
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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 zigzag 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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