RNAlib-2.1.9
+ 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
sequenceThe two sequences concatenated
structureWill 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_pA pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
c_pA pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
fML_pA 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_pA pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
fc_pA pointer to the 'fc' array, i.e. array ...
ggg_pA pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j]
indx_pA pointer to the indexing array used for accessing the energy matrices
ptype_pA 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_pA pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
c_pA pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
fML_pA 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_pA pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
fc_pA pointer to the 'fc' array, i.e. array ...
indx_pA pointer to the indexing array used for accessing the energy matrices
ptype_pA pointer to the ptype array containing the base pair types for each possibility (i,j)