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

2009/03/19 by Fenix W. D. Huang, Huang, Fenix W. D., Jing Qin +5
Biochemistry, Genetics and Molecular Biology · Mathematics · #05A16 #Combinatorics (math.CO) #FOS: Mathematics #Genomics and Chromatin Dynamics #RNA Research and Splicing #RNA and protein synthesis mechanisms #math.CO #msc:05A16

paper · pdf · doi:10.48550/arxiv.0903.3283

32 pages, 28 figures

arxiv created 2009/03/19 · openalex publication_date 2009/03/19 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

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 \citeBackhofen (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(N⁴M²)+O(N²M⁴) time and O(N²M²) space, where N,M denote the lengths of the interacting sequences.

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