MFE Structures of two hybridized Sequences
RNA Secondary Structure Prediction » Calculate Secondary Structures of two RNAs upon Dimerization RNA Secondary Structure Prediction » | Computing 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 | 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

  sequence | two RNA sequences separated by the '&' character
  structure | A 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

  sequence | The two sequences concatenated
  structure | Will 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_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
| ) |  |

`#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_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)

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

  e1 | A pointer to a variable where the energy of molecule A will be written to
  e2 | A 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

  vc | fold compound
  structure | Will hold the barcket dot structure of the dimer molecule

Returns
  minimum free energy of the structure