RNAexinv: A Tool for RNA Sequence Design
Author Information
Author(s): Avihoo Assaf, Churkin Alexander, Barash Danny
Primary Institution: Ben-Gurion University
Hypothesis
RNAexinv aims to design RNA sequences that not only fold into a desired structure but also exhibit favorable attributes such as thermodynamic stability and mutational robustness.
Conclusion
RNAexinv is a user-friendly tool that effectively designs RNA sequences while preserving their functional structures and improving their stability and robustness.
Supporting Evidence
- RNAexinv can be used without prior experience by simply specifying an RNA secondary structure.
- The tool generates sequences that adhere to the desired RNA shape while optimizing for stability and robustness.
- RNAexinv significantly reduces computation time compared to previous methods for the extended inverse RNA folding problem.
Takeaway
RNAexinv is like a smart helper that creates RNA sequences to match a specific shape while making sure they are strong and stable.
Methodology
The method involves using RNAinverse to find a good initial sequence, followed by a simulated annealing heuristic to refine the sequence based on shape, stability, and robustness.
Limitations
RNAexinv may take longer to compute results compared to simpler methods due to the complexity of the extended inverse RNA folding problem.
Digital Object Identifier (DOI)
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