Minimum Free Energy (MFE) Algorithms
Computing the Minimum Free Energy (MFE), i.e. the most stable conformation in thermodynamic equilibrium.
Specialized Modules:
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:
Global MFE Prediction - to compute the MFE for the entire sequence
Local (sliding window) MFE Prediction - to compute MFEs for each window using a sliding window approach
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.