Evolutionary solution for the RNA design problem

Abstract

Motivation: RNAs play fundamental roles in cellular processes. The function of an RNA is highly dependent on its 3D conformation, which is referred to as the RNA tertiary structure. Because the prediction or experimental determination of these structures is difficult, so many works focus on the problems associated with the RNA secondary structure. Here, we consider the RNA inverse folding problem, in which an RNA secondary structure is given as a target structure and the goal is to design an RNA sequence that folds into the target structure. In this article, we introduce a new evolutionary algorithm for the RNA inverse folding problem. Our algorithm, entitled Evolutionary RNA Design, generates a sequence whose minimum free energy structure is the same as the target structure. Results: We compare our algorithm with INFO-RNA, MODENA, RNAiFold and NUPACK approaches for some biological test sets. The results presented in this article indicate that for longer structures, our algorithm performs better than the other mentioned algorithms in terms of the energy range, accuracy, speedup and nucleotide distribution. Particularly, the generated RNA sequences in our method are much more reliable and similar to the natural RNA sequences. © The Author 2013. Published by Oxford University Press.