RNAlib-2.2.7
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Functions | |
float | vrna_Lfold (const char *string, int window_size, FILE *file) |
Local MFE prediction using a sliding window approach (simplified interface) More... | |
float | vrna_Lfoldz (const char *string, int window_size, double min_z, FILE *file) |
Local MFE prediction using a sliding window approach with z-score cut-off (simplified interface) More... | |
float | Lfold (const char *string, char *structure, int maxdist) |
The local analog to fold(). More... | |
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) |
Local MFE prediction using a sliding window approach. More... | |
float | vrna_mfe_window_zscore (vrna_fold_compound_t *vc, double min_z, FILE *file) |
Local MFE prediction using a sliding window approach (with z-score cut-off) More... | |
float vrna_Lfold | ( | const char * | string, |
int | window_size, | ||
FILE * | file | ||
) |
#include <ViennaRNA/Lfold.h>
Local MFE prediction using a sliding window approach (simplified interface)
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.
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) |
float vrna_Lfoldz | ( | const char * | string, |
int | window_size, | ||
double | min_z, | ||
FILE * | file | ||
) |
#include <ViennaRNA/Lfold.h>
Local MFE prediction using a sliding window approach with z-score cut-off (simplified interface)
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.
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) |
float Lfold | ( | const char * | string, |
char * | structure, | ||
int | maxdist | ||
) |
#include <ViennaRNA/Lfold.h>
The local analog to fold().
Computes the minimum free energy structure including only base pairs with a span smaller than 'maxdist'
float Lfoldz | ( | const char * | string, |
char * | structure, | ||
int | maxdist, | ||
int | zsc, | ||
double | min_z | ||
) |
#include <ViennaRNA/Lfold.h>
float vrna_mfe_window | ( | vrna_fold_compound_t * | vc, |
FILE * | file | ||
) |
#include <ViennaRNA/mfe.h>
Local MFE prediction using a sliding window approach.
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.
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 | ||
) |
#include <ViennaRNA/mfe.h>
Local MFE prediction using a sliding window approach (with z-score cut-off)
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.
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) |