aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights

Abstract

Abstract Background We study in this work the inverse folding problem for RNA, which is the discovery of sequences that fold into given target secondary structures. Results We implement a Lévy mutation scheme in an updated version of an evolutionary inverse folding algorithm and apply it to the design of RNAs with and without pseudoknots. We find that the Lévy mutation scheme increases the diversity of designed RNA sequences and reduces the average number of evaluations of the evolutionary algorithm. Compared to , CPU time is higher but more successful in finding designed sequences that fold correctly into the target structures. Conclusion We propose that a Lévy flight offers a better standard mutation scheme for optimizing RNA design. Our new version of is available on GitHub as a python script and the benchmark results show improved performance on both and the datasets, compared to existing inverse folding tools.