- Secondary Structure Prediction
- Tertiary Structure Prediction
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RNA structure prediction is powered by Fold tool in RNAstructure package. The structure score of the ith base can be converted to a pseudo-free energy according to this formula (Katherine et al.):
ΔGscore(i) = slope * ln[score(i)+1] + intercept
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RNA structure prediction is powered by SimRNA. Secondary structure is used as a restraint, and SHAPE scores can be used to generate secondary structure using RNAstructure package (Intercept=-0.6, Slop=1.8).