Minimum Free Energy Algorithm(s)

Table of Contents

• Zuker's Algorithm
• MFE for circular RNAs
• MFE Algorithm API

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 & Stiegler (1981)" [26].

MFE for circular RNAs

Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [10] for further details.

MFE Algorithm API

We provide interfaces for the prediction of

• MFE and corresponding secondary structure for single sequences,
• consensus MFE structures of sequence alignments, and
• MFE structure for two hybridized RNA strands

See also

Minimum Free Energy (MFE) Algorithms, consensus_mfe_fold, mfe_cofold, Computing MFE representatives of a Distance Based Partitioning

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