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

TL;DR

This paper introduces a new algorithm for predicting RNA-RNA interactions by computing the partition function and base pairing probabilities, improving understanding of antisense RNA and mRNA interactions.

Contribution

It derives the partition function for RNA-RNA interactions and presents the folding algorithm 'rip' with specific computational complexity.

Findings

The 'rip' algorithm computes partition functions and base pairing probabilities.

The algorithm operates in polynomial time with specified complexity.

Provides a tool for analyzing RNA interactions based on thermodynamic models.

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