// global functions float vrna_Lfold ( const char* string, int window_size, FILE* file ) float vrna_Lfoldz ( const char* string, int window_size, double min_z, FILE* file ) float Lfold ( const char* string, char* structure, int maxdist ) float Lfoldz ( const char* string, char* structure, int maxdist, int zsc, double min_z ) float vrna_mfe_window ( vrna_fold_compound_t* vc, FILE* file ) float vrna_mfe_window_zscore ( vrna_fold_compound_t* vc, double min_z, FILE* file )
float vrna_Lfold ( const char* string, int window_size, FILE* file )
This simplified interface to vrna_mfe_window() computes the MFE and locally optimal secondary structure using default options. Structures are predicted using a sliding window approach, where base pairs may not span outside the window. 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.
Parameters:
string | The nucleic acid sequence |
window_size | The window size for locally optimal structures |
file | The output file handle where predictions are written to (if NULL, output is written to stdout) |
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_window() , and the data structure vrna_fold_compound_t instead.
float vrna_Lfoldz ( const char* string, int window_size, double min_z, FILE* file )
This simplified interface to vrna_mfe_window_zscore() computes the MFE and locally optimal secondary structure using default options. Structures are predicted using a sliding window approach, where base pairs may not span outside the window. 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. This function is the z-score version of vrna_Lfold() , i.e. only predictions above a certain z-score cut-off value are printed.
Parameters:
string | The nucleic acid sequence |
window_size | The window size for locally optimal structures |
min_z | The minimal z-score for a predicted structure to appear in the output |
file | The output file handle where predictions are written to (if NULL, output is written to stdout) |
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_window() , and the data structure vrna_fold_compound_t instead.
float Lfold ( const char* string, char* structure, int maxdist )
Computes the minimum free energy structure including only base pairs with a span smaller than ‘maxdist’
Deprecated Use vrna_mfe_window() instead!
float Lfoldz ( const char* string, char* structure, int maxdist, int zsc, double min_z )
float vrna_mfe_window ( vrna_fold_compound_t* vc, FILE* file )
Computes minimum free energy structures using a sliding window approach, where base pairs may not span outside the window. In contrast to vrna_mfe() , where a maximum base pair span may be set using the vrna_md_t.max_bp_span attribute and one globally optimal structure is predicted, this function uses a sliding window to retrieve all locally optimal structures within each window. The size of the sliding window is set in the vrna_md_t.window_size attribute, prior to the retrieval of the vrna_fold_compound_t using vrna_fold_compound() with option VRNA_OPTION_WINDOW
The predicted structures are written on-the-fly, either to stdout, if a NULL pointer is passed as file parameter, or to the corresponding filehandle.
SWIG Wrapper Notes This function is attached as method mfe_window() to objects of type fold_compound
Parameters:
vc | The vrna_fold_compound_t with preallocated memory for the DP matrices |
file | The output file handle where predictions are written to (maybe NULL) |
float vrna_mfe_window_zscore ( vrna_fold_compound_t* vc, double min_z, FILE* file )
Computes minimum free energy structures using a sliding window approach, where base pairs may not span outside the window. This function is the z-score version of vrna_mfe_window() , i.e. only predictions above a certain z-score cut-off value are printed. As for vrna_mfe_window() , the size of the sliding window is set in the vrna_md_t.window_size attribute, prior to the retrieval of the vrna_fold_compound_t using vrna_fold_compound() with option VRNA_OPTION_WINDOW .
The predicted structures are written on-the-fly, either to stdout, if a NULL pointer is passed as file parameter, or to the corresponding filehandle.
Parameters:
vc | The vrna_fold_compound_t with preallocated memory for the DP matrices |
min_z | The minimal z-score for a predicted structure to appear in the output |
file | The output file handle where predictions are written to (maybe NULL) |