ViennaRNA
Posts tagged “ViennaRNA”.
ViennaRNA training and workshops for researchers, starting in 2027
A series of practical ViennaRNA training modules and workshops is in preparation at RNA Forecast, planned to begin in early 2027. The training is for researchers who use RNA structure prediction...
AI for RNA structure prediction: what deep learning models learn
What neural networks trained on known RNA structures actually learn, why the usual benchmarks overstate their accuracy, what a test on synthetic data revealed about their outputs, and what has changed since 2022.
RNAfold in practice: MFE, pair probabilities and ensemble in ViennaRNA
How to read the output of RNAfold in the ViennaRNA Package, i.e. the minimum free energy structure, the pair probabilities, the centroid and MEA structures, the suboptimal structures from RNAsubopt, and how to tell...
SHAPE and chemical probing data in RNA structure prediction: how to fold with reactivities in ViennaRNA
How SHAPE reactivities go into RNAfold, what the three methods in ViennaRNA do with them, and what probing data change in a prediction and what they do not. Worked example with yeast tRNA-Phe, all commands included.
Deep learning for RNA secondary structure prediction: the caveats
This paper shows that many deep learning models for RNA secondary structure prediction learn dataset bias more readily than RNA folding rules, and explains why that matters for the future of AI in RNA biology.