A Combinatorial Approach for Multiple RNA Interaction: Formulations, Approximations, and Heuristics

Abstract

AbstractThe interaction of two RNA molecules involves a complex interplay between folding and binding that warranted recent developments in RNA-RNA interaction algorithms. However, biological mechanisms in which more than two RNAs take part in an interaction exist.We formulate multiple RNA interaction as a computational problem, which not surprisingly turns out to be NP-complete. Our experiments with approximation algorithms and heuristics for the problem suggest that this formulation is indeed useful to determine interaction patterns of multiple RNAs when information about which RNAs interact is not necessarily available (as opposed to the case of two RNAs where one must interact with the other), and because the resulting RNA structure often cannot be predicated by existing algorithms when RNAs are simply handled in pairs. We show instances of multiple RNA interaction that are accurately predicted by our algorithms.Keywordsmultiple RNA interactiondynamic programmingapproximation algorithmsstructure prediction