Minimum Free Energy (MFE) Algorithms

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

Detailed Description

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
• 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.

Collaboration diagram for Minimum Free Energy (MFE) Algorithms:

Modules
	Global MFE Prediction
	Variations of the global Minimum Free Energy (MFE) prediction algorithm.
	Local (sliding window) MFE Prediction
	Variations of the local (sliding window) Minimum Free Energy (MFE) prediction algorithm.
	Backtracking MFE structures
	Backtracking related interfaces.

Files
file	mfe.h
	Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data.
file	mfe_window.h
	Compute local Minimum Free Energy (MFE) using a sliding window approach and backtrace corresponding secondary structures.