Variations of the global Minimum Free Energy (MFE) prediction algorithm. More...

Detailed Description

Variations of the global Minimum Free Energy (MFE) prediction algorithm.

We provide implementations of the global MFE prediction algorithm for

Single sequences,
Multiple sequence alignments (MSA), and
RNA-RNA hybrids

Collaboration diagram for Global MFE Prediction:

Modules
	Computing 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.

	Deprecated Interface for Global MFE Prediction

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

Basic global MFE prediction interface
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...

float	vrna_mfe_dimer (vrna_fold_compound_t vc, char structure)
	Compute the minimum free energy of two interacting RNA molecules. More...

Simplified global MFE prediction using sequence(s) or multiple sequence alignment(s)
float	vrna_fold (const char sequence, char structure)
	Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence. More...

float	vrna_circfold (const char sequence, char structure)
	Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequence. More...

float	vrna_alifold (const char *sequences, char structure)
	Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA sequence alignment using a comparative method. More...

float	vrna_circalifold (const char *sequences, char structure)
	Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence alignment of circular RNAs using a comparative method. More...

float	vrna_cofold (const char sequence, char structure)
	Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences. More...

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

vc	fold compound
structure	A 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

float vrna_mfe_dimer	(	vrna_fold_compound_t *	vc,
		char *	structure
	)

#include <ViennaRNA/mfe.h>

Compute the minimum free energy of two interacting RNA molecules.

The code is analog to the vrna_mfe() function.

Parameters

vc	fold compound
structure	Will hold the barcket dot structure of the dimer molecule

Returns: minimum free energy of the structure

SWIG Wrapper Notes:: This function is attached as method mfe_dimer() to objects of type fold_compound

float vrna_fold	(	const char *	sequence,
		char *	structure
	)

#include <ViennaRNA/mfe.h>

Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence.

This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for an RNA sequence using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.

Note: In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use vrna_mfe(), and the data structure vrna_fold_compound_t instead.

See also: vrna_circfold(), vrna_mfe()

Parameters

sequence	RNA sequence
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns: the minimum free energy (MFE) in kcal/mol

float vrna_circfold	(	const char *	sequence,
		char *	structure
	)

#include <ViennaRNA/mfe.h>

Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequence.

This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for a circular RNA sequence using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.

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

Note: In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use vrna_mfe(), and the data structure vrna_fold_compound_t instead.

See also: vrna_fold(), vrna_mfe()

Parameters

sequence	RNA sequence
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns: the minimum free energy (MFE) in kcal/mol

float vrna_alifold	(	const char **	sequences,
		char *	structure
	)

#include <ViennaRNA/mfe.h>

Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA sequence alignment using a comparative method.

This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary structure for an RNA sequence alignment using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.

Note: In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use vrna_mfe(), and the data structure vrna_fold_compound_t instead.

See also: vrna_circalifold(), vrna_mfe()

Parameters

sequences	RNA sequence alignment
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns: the minimum free energy (MFE) in kcal/mol

float vrna_circalifold	(	const char **	sequences,
		char *	structure
	)

#include <ViennaRNA/mfe.h>

Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence alignment of circular RNAs using a comparative method.

This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary structure for an RNA sequence alignment using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.

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

Note: In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use vrna_mfe(), and the data structure vrna_fold_compound_t instead.

See also: vrna_alifold(), vrna_mfe()

Parameters

sequences	Sequence alignment of circular RNAs
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns: the minimum free energy (MFE) in kcal/mol

float vrna_cofold	(	const char *	sequence,
		char *	structure
	)

#include <ViennaRNA/mfe.h>

Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences.

This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for two RNA sequences upon dimerization using default options. Memory required for dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.

Note: In case you want to use the filled DP matrices for any subsequent post-processing step, or you require other conditions than specified by the default model details, use vrna_mfe(), and the data structure vrna_fold_compound_t instead.

See also: vrna_mfe_dimer(), vrna_fold_compound(), vrna_fold_compound_t, vrna_cut_point_insert()

Parameters

sequence	two RNA sequences separated by the '&' character
structure	A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns: the minimum free energy (MFE) in kcal/mol

Detailed Description

Modules

Files

Basic global MFE prediction interface

Simplified global MFE prediction using sequence(s) or multiple sequence alignment(s)

Function Documentation