RNAlib-2.2.7
+ Collaboration diagram for MFE Structures of two hybridized Sequences:

Files

file  cofold.h
 MFE version of cofolding routines.
 

Functions

float vrna_cofold (const char *string, char *structure)
 Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences. More...
 
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, vrna_param_t *parameters, int is_constrained)
 Compute the minimum free energy of two interacting RNA molecules. More...
 
void free_co_arrays (void)
 Free memory occupied by cofold() More...
 
void update_cofold_params (void)
 Recalculate parameters. More...
 
void update_cofold_params_par (vrna_param_t *parameters)
 Recalculate parameters. More...
 
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...
 
void get_monomere_mfes (float *e1, float *e2)
 get_monomer_free_energies More...
 
void initialize_cofold (int length)
 
float vrna_mfe_dimer (vrna_fold_compound_t *vc, char *structure)
 Compute the minimum free energy of two interacting RNA molecules. More...
 

Detailed Description

Function Documentation

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

#include <ViennaRNA/cofold.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
sequencetwo RNA sequences separated by the '&' character
structureA 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 cofold ( const char *  sequence,
char *  structure 
)

#include <ViennaRNA/cofold.h>

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().

Deprecated:
use vrna_mfe_dimer() instead
Parameters
sequenceThe two sequences concatenated
structureWill hold the barcket dot structure of the dimer molecule
Returns
minimum free energy of the structure
float cofold_par ( const char *  string,
char *  structure,
vrna_param_t parameters,
int  is_constrained 
)

#include <ViennaRNA/cofold.h>

Compute the minimum free energy of two interacting RNA molecules.

Deprecated:
use vrna_mfe_dimer() instead
void free_co_arrays ( void  )

#include <ViennaRNA/cofold.h>

Free memory occupied by cofold()

Deprecated:
This function will only free memory allocated by a prior call of cofold() or cofold_par(). See vrna_mfe_dimer() for how to use the new API
Note
folding matrices now reside in the fold compound, and should be free'd there
See also
vrna_fc_destroy(), vrna_mfe_dimer()
void update_cofold_params ( void  )

#include <ViennaRNA/cofold.h>

Recalculate parameters.

Deprecated:
See vrna_params_subst() for an alternative using the new API
void update_cofold_params_par ( vrna_param_t parameters)

#include <ViennaRNA/cofold.h>

Recalculate parameters.

Deprecated:
See vrna_params_subst() for an alternative using the new API
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 
)

#include <ViennaRNA/cofold.h>

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

Deprecated:
folding matrices now reside within the fold compound. Thus, this function will only work in conjunction with a prior call to cofold() or cofold_par()
See also
vrna_mfe_dimer() for the new API
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 
)

#include <ViennaRNA/cofold.h>

Export the arrays of partition function cofold.

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

Deprecated:
folding matrices now reside within the vrna_fold_compound_t. Thus, this function will only work in conjunction with a prior call to the deprecated functions cofold() or cofold_par()
See also
vrna_mfe_dimer() for the new API
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)
void get_monomere_mfes ( float *  e1,
float *  e2 
)

#include <ViennaRNA/cofold.h>

get_monomer_free_energies

Export monomer free energies out of cofold arrays

Deprecated:
{This function is obsolete and will be removed soon!}
Parameters
e1A pointer to a variable where the energy of molecule A will be written to
e2A pointer to a variable where the energy of molecule B will be written to
void initialize_cofold ( int  length)

#include <ViennaRNA/cofold.h>

allocate arrays for folding

Deprecated:
{This function is obsolete and will be removed soon!}
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
vcfold compound
structureWill hold the barcket dot structure of the dimer molecule
Returns
minimum free energy of the structure