期刊
JOURNAL OF MATHEMATICAL BIOLOGY
卷 64, 期 3, 页码 529-556出版社
SPRINGER
DOI: 10.1007/s00285-011-0423-7
关键词
RNA-RNA interaction; Joint structure; Shape; Symbolic enumeration; Singularity analysis
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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