aRNAque: Evolutionary Algorithm for Inverse RNA Folding

Authors: Merleau NSC, Smerlak M

Published in: BMC Bioinformatics (2022)

Citations: 18

Abstract:
The inverse RNA folding problem — designing a sequence that folds into a target secondary structure — is computationally challenging, especially for pseudoknots. aRNAque introduces an evolutionary algorithm inspired by Lévy flight random walks, mixing small local and rare large mutations. Benchmarked on the Pseudobase++ dataset, aRNAque achieves state-of-the-art performance on pseudoknot design while remaining competitive on standard structures, demonstrating that heavy-tailed mutation distributions are effective for navigating RNA fitness landscapes.