MoiRNAiFold: a novel tool for complex in silico RNA design.

Nucleic Acids Res

Moirai Biodesign, c/ Baldiri Reixach s/n, Parc Científic de Barcelona (PCB), 08028 Barcelona, Spain.

Published: May 2021

AI Article Synopsis

  • Rapid and cost-effective tools for designing synthetic RNA constructs like riboregulators are essential for advancing diagnostics and therapies.
  • MoiRNAiFold is a new, user-friendly software that utilizes Constraint Programming and innovative strategies to efficiently design RNA, handling multiple constraints and improving gene expression regulation features.
  • Proven effective through benchmarking and real-world testing, MoiRNAiFold produces functional RNA sequences, is available for free online, and outperforms previous design software.

Article Abstract

Novel tools for in silico design of RNA constructs such as riboregulators are required in order to reduce time and cost to production for the development of diagnostic and therapeutic advances. Here, we present MoiRNAiFold, a versatile and user-friendly tool for de novo synthetic RNA design. MoiRNAiFold is based on Constraint Programming and it includes novel variable types, heuristics and restart strategies for Large Neighborhood Search. Moreover, this software can handle dozens of design constraints and quality measures and improves features for RNA regulation control of gene expression, such as Translation Efficiency calculation. We demonstrate that MoiRNAiFold outperforms any previous software in benchmarking structural RNA puzzles from EteRNA. Importantly, with regard to biologically relevant RNA designs, we focus on RNA riboregulators, demonstrating that the designed RNA sequences are functional both in vitro and in vivo. Overall, we have generated a powerful tool for de novo complex RNA design that we make freely available as a web server (https://moiraibiodesign.com/design/).

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136780PMC
http://dx.doi.org/10.1093/nar/gkab331DOI Listing

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