RNAlib-2.3.1
Minimum Free Energy (MFE) algorithms

Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data. More...

+ Collaboration diagram for Minimum Free Energy (MFE) algorithms:

Modules

 MFE Consensus Structures for Sequence Alignment(s)
 
 Calculating MFE representatives of a Distance Based Partitioning
 Compute the minimum free energy (MFE) and secondary structures for a partitioning of the secondary structure space according to the base pair distance to two fixed reference structures basepair distance to two fixed reference structures.
 
 MFE Structures of single Nucleic Acid Sequences
 This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences.
 
 MFE Structures of two hybridized Sequences
 MFE version of cofolding routines This file includes (almost) all function declarations within the RNAlib that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines.
 
 Local MFE structure Prediction and Z-scores
 

Files

file  fold.h
 MFE calculations for single RNA sequences.
 

Functions

float vrna_mfe (vrna_fold_compound_t *vc, char *structure)
 Compute minimum free energy and an appropriate secondary structure of an RNA sequence, or RNA sequence alignment. More...
 

Detailed Description

Compute Minimum Free energy (MFE) and backtrace corresponding secondary structures from RNA sequence data.

The library provides a fast dynamic programming minimum free energy folding algorithm as described in [23]. All relevant parts that directly implement the "Zuker & Stiegler" algorithm for single sequences are described in this section.

Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [7] for further details.

Nevertheless, the RNAlib also provides interfaces for the prediction of consensus MFE structures of sequence alignments, MFE structure for two hybridized sequences, local optimal structures and many more. For those more specialized variants of MFE folding routines, please consult the appropriate subsections (Modules) as listed above.

Function Documentation

float vrna_mfe ( vrna_fold_compound_t vc,
char *  structure 
)

#include <ViennaRNA/mfe.h>

Compute minimum free energy and an appropriate secondary structure of an RNA sequence, or RNA sequence alignment.

Depending on the type of the provided vrna_fold_compound_t, this function predicts the MFE for a single sequence, or a corresponding averaged MFE for a sequence alignment. If backtracking is activated, it also constructs the corresponding secondary structure, or consensus structure. Therefore, the second parameter, structure, has to point to an allocated block of memory with a size of at least $\mathrm{strlen}(\mathrm{sequence})+1$ to store the backtracked MFE structure. (For consensus structures, this is the length of the alignment + 1. If NULL is passed, no backtracking will be performed.

Note
This function is polymorphic. It accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE, and VRNA_FC_TYPE_COMPARATIVE.
See also
vrna_fold_compound_t, vrna_fold_compound(), vrna_fold(), vrna_circfold(), vrna_fold_compound_comparative(), vrna_alifold(), vrna_circalifold()
Parameters
vcfold compound
structureA pointer to the character array where the secondary structure in dot-bracket notation will be written to (Maybe NULL)
Returns
the minimum free energy (MFE) in kcal/mol
SWIG Wrapper Notes:
This function is attached as method mfe() to objects of type fold_compound