RNA folding

RNAs are molecules that are essential to any living organism. The minimum free-energy (MFE) structure represents the most stable structure among all of the structures adopted by a sequence. The suboptimal backtrack can be adapted to any algorithm based on an unambiguous dynamic programming scheme. It remains valid for an ambiguous decomposition, albeit generating some structures redundantly. Comparative folding represents a final category of methods for structure prediction. Since the logarithm is a monotonously increasing function, optimizing the logarithm of the objective function is equivalent to optimizing the objective function. The principle behind the Sankoff algorithm is at the core of virtually every approach for comparative prediction. The partition function is essential to adopt a statistical perspective over the Boltzmann ensemble. The partition function is an essential quantity to derive the statistical properties of the folding space.