Minimum Free Energy (MFE) Algorithms

Computing the Minimum Free Energy (MFE), i.e. the most stable conformation in thermodynamic equilibrium.

Zuker’s Algorithm

Our library provides fast dynamic programming Minimum Free Energy (MFE) folding algorithms derived from the decomposition scheme as described by Zuker and Stiegler [1981].

MFE for circular RNAs

Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See Hofacker and Stadler [2006] for further details.

MFE Algorithm API

Predicting the Minimum Free Energy (MFE) and a corresponding (consensus) secondary structure.

In a nutshell we provide two different flavors for MFE prediction:

Each of these flavors, again, provides two implementations to either compute the MFE based on

  • single RNA (DNA) sequence(s), or

  • multiple sequences interacting with each other, or

  • a comparative approach using multiple sequence alignments (MSA).

For the latter, a consensus secondary structure is predicted and our implementations compute an average of free energies for each sequence in the MSA plus an additional covariance pseudo-energy term.

The implementations for Backtracking MFE structures are generally agnostic with respect to whether local or global structure prediction is in place.