aRNAque

aRNAque addresses the inverse RNA folding problem by identifying nucleotide sequences that fold into specified target secondary structures, including pseudoknots.

Key Features:

• Lévy flight-inspired mutation scheme: Implements mutations based on Lévy flights, with step lengths drawn from a heavy-tailed distribution, to enhance exploration and diversity of candidate RNA sequences.
• Pseudoknot handling: Designs sequences that fold into secondary structures containing pseudoknots, i.e., non-nested base-pairing interactions.
• Performance optimization: The Lévy mutation scheme reduces the average number of evaluations required for successful designs while potentially increasing CPU time relative to tools such as antaRNA, and yields a higher success rate in generating target folds.
• Benchmarking: Evaluated against datasets including Pseudobase++ and Eterna100, demonstrating improved performance over other inverse folding algorithms.

Scientific Applications:

• RNA design: Generating novel nucleotide sequences that fold into specified secondary structures for functional studies or therapeutic design.
• Structural biology: Investigating folding and stability of RNAs with complex secondary structures, including pseudoknots.
• Evolutionary studies: Exploring sequence-space and evolutionary trajectories that lead to particular RNA structural phenotypes.

Methodology:

aRNAque uses an iterative evolutionary algorithm in which candidate sequences undergo mutation, selection, and recombination, and applies Lévy flight-inspired mutation schemes to enable both local refinements and broader exploration of the sequence landscape.