MFE Structures of two hybridized Sequences
[Calculate Secondary Structures of two RNAs upon Dimerization, Calculating Minimum Free Energy (MFE) Structures]

Collaboration diagram for MFE Structures of two hybridized Sequences:

Files
file	cofold.h
	MFE version of cofolding routines.
Functions
float	cofold (const char *sequence, char *structure)
	Compute the minimum free energy of two interacting RNA molecules.
float	cofold_par (const char *string, char *structure, paramT *parameters, int is_constrained)
	Compute the minimum free energy of two interacting RNA molecules.
void	free_co_arrays (void)
	Free memory occupied by cofold().
void	update_cofold_params (void)
	Recalculate parameters.
void	export_cofold_arrays_gq (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **ggg_p, int **indx_p, char **ptype_p)
	Export the arrays of partition function cofold (with gquadruplex support).
void	export_cofold_arrays (int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **fc_p, int **indx_p, char **ptype_p)
	Export the arrays of partition function cofold.

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Function Documentation

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

Compute the minimum free energy of two interacting RNA molecules.

The code is analog to the fold() function. If cut_point ==-1 results should be the same as with fold().

Parameters:

	sequence	The two sequences concatenated
	structure	Will hold the barcket dot structure of the dimer molecule

Returns:

minimum free energy of the structure

void export_cofold_arrays_gq	(	int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	fc_p,
		int **	ggg_p,
		int **	indx_p,
		char **	ptype_p
	)

Export the arrays of partition function cofold (with gquadruplex support).

Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking

Parameters:

	f5_p	A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
	c_p	A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
	fML_p	A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
	fM1_p	A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
	fc_p	A pointer to the 'fc' array, i.e. array ...
	ggg_p	A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j]
	indx_p	A pointer to the indexing array used for accessing the energy matrices
	ptype_p	A pointer to the ptype array containing the base pair types for each possibility (i,j)

void export_cofold_arrays	(	int **	f5_p,
		int **	c_p,
		int **	fML_p,
		int **	fM1_p,
		int **	fc_p,
		int **	indx_p,
		char **	ptype_p
	)

Export the arrays of partition function cofold.

Export the cofold arrays for use e.g. in the concentration Computations or suboptimal secondary structure backtracking

Parameters:

	f5_p	A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
	c_p	A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
	fML_p	A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
	fM1_p	A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
	fc_p	A pointer to the 'fc' array, i.e. array ...
	indx_p	A pointer to the indexing array used for accessing the energy matrices
	ptype_p	A pointer to the ptype array containing the base pair types for each possibility (i,j)