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

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

2009-03-19

arxiv.org/abs/0903.3283v1

Mathematics

Combinatorics

32 pages, 28 figures

Scientific paper

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 $O(N^4M^2)+O(N^2M^4)$ time and $O(N^2M^2)$ space, where $N,M$ denote the lengths of the interacting sequences.

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