Biomaterial Database

aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights. 2022

Nono S C Merleau, and Matteo Smerlak

Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, 04103, Leipzig, Germany. nonosaha@mis.mpg.de.

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 aRNAque 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 antaRNA, aRNAque CPU time is higher but more successful in finding designed sequences that fold correctly into the target structures. CONCLUSIONS We propose that a Lévy flight offers a better standard mutation scheme for optimizing RNA design. Our new version of aRNAque is available on GitHub as a python script and the benchmark results show improved performance on both Pseudobase++ and the Eterna100 datasets, compared to existing inverse folding tools.

UI	MeSH Term	Description	Entries
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D000465	Algorithms	A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.	Algorithm
D012313	RNA	A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)	RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated
D017423	Sequence Analysis, RNA	A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.	RNA Sequence Analysis,Sequence Determination, RNA,Analysis, RNA Sequence,Determination, RNA Sequence,Determinations, RNA Sequence,RNA Sequence Determination,RNA Sequence Determinations,RNA Sequencing,Sequence Determinations, RNA,Analyses, RNA Sequence,RNA Sequence Analyses,Sequence Analyses, RNA,Sequencing, RNA
D059370	RNA Folding	The processes of RNA tertiary structure formation.	RNA Refolding,RNA Unfolding,Folding, RNA,Foldings, RNA,RNA Foldings,RNA Refoldings,RNA Unfoldings,Refolding, RNA,Refoldings, RNA,Unfolding, RNA,Unfoldings, RNA