This module contains all functions and variables related to the calculation of global minimum free energy structures for single sequences. More…
// global functions float vrna_fold ( const char* sequence, char* structure ) float vrna_circfold ( const char* sequence, char* structure ) float fold_par ( const char* sequence, char* structure, vrna_param_t* parameters, int is_constrained, int is_circular ) float fold ( const char* sequence, char* structure ) float circfold ( const char* sequence, char* structure ) void free_arrays (void) void update_fold_params (void) void update_fold_params_par (vrna_param_t* parameters) void export_fold_arrays ( int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p ) void export_fold_arrays_par ( int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p, vrna_param_t** P_p ) void export_circfold_arrays ( int* Fc_p, int* FcH_p, int* FcI_p, int* FcM_p, int** fM2_p, int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p ) void export_circfold_arrays_par ( int* Fc_p, int* FcH_p, int* FcI_p, int* FcM_p, int** fM2_p, int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p, vrna_param_t** P_p ) int LoopEnergy ( int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1 ) int HairpinE ( int size, int type, int si1, int sj1, const char* string ) void initialize_fold (int length) char* backtrack_fold_from_pair ( char* sequence, int i, int j )
float vrna_fold ( const char* sequence, char* structure )
This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for an RNA sequence 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.
Parameters:
sequence | RNA sequence |
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
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_circfold() , vrna_mfe() , vrna_fold_compound() , vrna_fold_compound_t
float vrna_circfold ( const char* sequence, char* structure )
This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for a circular RNA sequence 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.
Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [7] for further details.
Parameters:
sequence | RNA sequence |
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
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_fold() , vrna_mfe() , vrna_fold_compound() , vrna_fold_compound_t
float fold_par ( const char* sequence, char* structure, vrna_param_t* parameters, int is_constrained, int is_circular )
The first parameter given, the RNA sequence, must be uppercase and should only contain an alphabet \(\Sigma\) that is understood by the RNAlib
(e.g. :math:` Sigma = {A,U,C,G} ` )
The second parameter, structure , must always point to an allocated block of memory with a size of at least \(\mathrm{strlen}(\mathrm{sequence})+1\)
If the third parameter is NULL, global model detail settings are assumed for the folding recursions. Otherwise, the provided parameters are used.
The fourth parameter indicates whether a secondary structure constraint in enhanced dot-bracket notation is passed through the structure parameter or not. If so, the characters ” | x < > ” are recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively. Matching brackets ” ( ) ” denote base pairs, dots “.” are used for unconstrained bases.
To indicate that the RNA sequence is circular and thus has to be post-processed, set the last parameter to non-zero
After a successful call of fold_par() , a backtracked secondary structure (in dot-bracket notation) that exhibits the minimum of free energy will be written to the memory structure is pointing to. The function returns the minimum of free energy for any fold of the sequence given.
Deprecated use vrna_mfe() instead!
Parameters:
sequence | RNA sequence |
structure | A pointer to the character array where the secondary structure in dot-bracket notation will be written to |
parameters | A data structure containing the pre-scaled energy contributions and the model details. (NULL may be passed, see OpenMP notes above) |
is_constrained | Switch to indicate that a structure constraint is passed via the structure argument (0==off) |
is_circular | Switch to (de-)activate post-processing steps in case RNA sequence is circular (0==off) |
Returns:
the minimum free energy (MFE) in kcal/mol
Note
OpenMP: Passing NULL to the ‘parameters’ argument involves access to several global model detail variables and thus is not to be considered threadsafe
See also:
vrna_mfe() , fold() , circfold() , vrna_md_t , set_energy_model(), get_scaled_parameters()
float fold ( const char* sequence, char* structure )
This function essentially does the same thing as fold_par() . However, it takes its model details, i.e. temperature , dangles , tetra_loop , noGU , no_closingGU , fold_constrained , noLonelyPairs from the current global settings within the library
Deprecated use vrna_fold() , or vrna_mfe() instead!
Parameters:
sequence | RNA sequence |
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
See also:
float circfold ( const char* sequence, char* structure )
This function essentially does the same thing as fold_par() . However, it takes its model details, i.e. temperature , dangles , tetra_loop , noGU , no_closingGU , fold_constrained , noLonelyPairs from the current global settings within the library
Deprecated Use vrna_circfold() , or vrna_mfe() instead!
Parameters:
sequence | RNA sequence |
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
See also:
void free_arrays (void)
void update_fold_params (void)
void update_fold_params_par (vrna_param_t* parameters)
void export_fold_arrays ( int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p )
void export_fold_arrays_par ( int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p, vrna_param_t** P_p )
void export_circfold_arrays ( int* Fc_p, int* FcH_p, int* FcI_p, int* FcM_p, int** fM2_p, int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p )
void export_circfold_arrays_par ( int* Fc_p, int* FcH_p, int* FcI_p, int* FcM_p, int** fM2_p, int** f5_p, int** c_p, int** fML_p, int** fM1_p, int** indx_p, char** ptype_p, vrna_param_t** P_p )
int LoopEnergy ( int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1 )
int HairpinE ( int size, int type, int si1, int sj1, const char* string )
void initialize_fold (int length)
Allocate arrays for folding
Deprecated See vrna_mfe() and vrna_fold_compound_t for the usage of the new API!