RNA-RNA interaction prediction: partition function and base pair pairing probabilities

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

Publication date 19 March 2009

Abstract: In this paper, we study the interaction of an antisense RNA and its target mRNA, based on the model introduced by Alkan {it et al.} (Alkan {it et al.}, J. Comput. Biol., Vol:267--282, 2006). Our main results are the derivation of the partition function cite{Backhofen} (Chitsaz {it et al.}, Bioinformatics, to appear, 2009), based on the concept of tight-structure and the computation of the base pairing probabilities. This paper contains the folding algorithm {sf rip} which computes the partition function as well as the base pairing probabilities in

O (N^{4} M^{2}) + O (N^{2} M^{4})

time and

O (N^{2} M^{2})

space, where

N, M

denote the lengths of the interacting sequences.

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