ARNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Levy flights.

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 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.

Conclusion

We propose that a Lévy flight offers a better standard mutation scheme for optimizing RNA design. Our new version of

SUBMITTER: Merleau NSC 

PROVIDER: S-EPMC9375295 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature