Rna-rna Interaction Prediction: Partition Function and Base Pair Pairing Probabilities
نویسندگان
چکیده
In this paper, we study the interaction of an antisense RNA and its target mRNA, based on the model introduced by Alkan et al. (Alkan et al., J. Comput. Biol., Vol:267–282, 2006). Our main results are the derivation of the partition function [11] (Chitsaz 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 rip which computes the partition function as well as the base pairing probabilities in O(NM) + O(NM) time and O(NM) space, where N, M denote the lengths of the interacting sequences. RNA-RNA interaction, joint structure, dynamic programming, partition function, base pairing probability, loop, RNA secondary structure.
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تاریخ انتشار 2009