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

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dc.creatorHuang, Fenix W. D.
dc.creatorQin, Jing
dc.creatorReidys, Christian M.
dc.creatorStadler, Peter F.
dc.date2009-03-19
dc.date.accessioned2026-07-07T12:54:13Z
dc.date.available2026-07-07T12:54:13Z
dc.descriptionIn 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.
dc.description32 pages, 28 figures
dc.identifierhttps://arxiv.org/abs/0903.3283
dc.identifierhttp://arxiv.org/abs/0903.3283
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/223856
dc.subjectCombinatorics
dc.subject05A16
dc.titleRNA-RNA interaction prediction: partition function and base pair pairing probabilities
dc.typetext

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