Journal Article

Partition function and base pairing probabilities for RNA–RNA interaction prediction

Fenix W. D. Huang, Jing Qin, Christian M. Reidys and Peter F. Stadler

in Bioinformatics

Volume 25, issue 20, pages 2646-2654
Published in print October 2009 | ISSN: 1367-4803
Published online August 2009 | e-ISSN: 1460-2059 | DOI:
Partition function and base pairing probabilities for RNA–RNA interaction prediction

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Motivation: The RNA–RNA interaction problem (RIP) consists in finding the energetically optimal structure of two RNA molecules that bind to each other. The standard model allows secondary structures in both partners as well as additional base pairs between the two RNAs subject to certain restrictions that ensure that RIP is solvabale by a polynomial time dynamic programming algorithm. RNA–RNA binding, like RNA folding, is typically not dominated by the ground state structure. Instead, a large ensemble of alternative structures contributes to the interaction thermodynamics.

Results: We present here an O(N6) time and O(N4) dynamics programming algorithm for computing the full partition function for RIP which is based on the combinatorial notion of ‘tight structures’. Albeit equivalent to recent work by H. Chitsaz and collaborators, our approach in addition provides a full-fledged computation of the base pairing probabilities, which relies on the notion of a decomposition tree for joint structures. In practise, our implementation is efficient enough to investigate, for instance, the interactions of small bacterial RNAs and their target mRNAs.

Availability: The program rip is implemented in C. The source code is available for download from and


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6807 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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