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Design of RNAs: comparing programs for inverse RNA folding
Alexander Churkin1, Matan Drory Retwitzer2, Vladimir Reinharz2,3
1Shamoon College of Engineering and Physics Department at Ben-Gurion University, Beer-Sheva, Israel.
Briefings in Bioinformatics
|January 4, 2017
Summary
Inverse RNA folding computational programs predict RNA sequences for desired structures. This review compares popular freeware tools like RNAinverse, antaRNA, RNAiFold, and incaRNAfbinv for RNA design and noncoding RNA detection.
Area of Science:
- Computational Biology
- Molecular Biology
- Bioinformatics
Background:
- Computational programs for predicting RNA sequences with specific folding properties have advanced significantly.
- Inverse RNA folding predicts sequences that fold into a target minimum free energy secondary structure under various constraints.
Purpose of the Study:
- This review describes and compares popular freeware programs for inverse RNA folding.
- The goal is to aid practitioners in selecting suitable programs for RNA design tasks.
Main Methods:
- The review covers established programs like RNAinverse and newer tools such as antaRNA, RNAiFold, and incaRNAfbinv.
- It discusses diverse computational approaches including ant colony optimization, constraint programming, adaptive walk, simulated annealing, and Boltzmann sampling.
Main Results:
- The described programs offer distinct features beneficial for specific biological problems.
- A comparison of these programs and their methodologies is provided.
Conclusions:
- Inverse RNA folding is crucial for designing optimized RNAs in synthetic biology and RNA nanostructures.
- It also serves as a valuable preprocessing step for detecting novel noncoding RNAs.
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