MFE Structures of two hybridized Sequences

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. More...
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) More...
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. More...

Detailed Description

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)