RNAlib-2.3.1
MFE Structures of two hybridized Sequences

MFE version of cofolding routines This file includes (almost) all function declarations within the RNAlib that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines. More...

+ Collaboration diagram for MFE Structures of two hybridized Sequences:

Functions

float vrna_cofold (const char *sequence, 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

MFE version of cofolding routines This file includes (almost) all function declarations within the RNAlib that are related to MFE Cofolding... This also includes the Zuker suboptimals calculations, since they are implemented using the cofold routines.

Function Documentation

float vrna_cofold ( const char *  sequence,
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
SWIG Wrapper Notes:
This function is attached as method mfe_dimer() to objects of type fold_compound