RNAlib-2.2.7
+ Collaboration diagram for Local MFE structure Prediction and Z-scores:

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...
 

Detailed Description

Function Documentation

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.

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.
See also
vrna_mfe_window(), vrna_Lfoldz(), vrna_mfe_window_zscore(), vrna_fold_compound(), vrna_fold_compound_t
Parameters
stringThe nucleic acid sequence
window_sizeThe window size for locally optimal structures
fileThe 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.

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.
See also
vrna_mfe_window_zscore(), vrna_Lfold(), vrna_mfe_window(), vrna_fold_compound(), vrna_fold_compound_t
Parameters
stringThe nucleic acid sequence
window_sizeThe window size for locally optimal structures
min_zThe minimal z-score for a predicted structure to appear in the output
fileThe 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'

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 
)

#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.

See also
vrna_fold_compound(), vrna_mfe_window_zscore(), vrna_mfe(), vrna_Lfold(), vrna_Lfoldz(), #VRNA_OPTION_WINDOW, vrna_md_t.max_bp_span, vrna_md_t.window_size
Parameters
vcThe vrna_fold_compound_t with preallocated memory for the DP matrices
fileThe 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.

See also
vrna_fold_compound(), vrna_mfe_window_zscore(), vrna_mfe(), vrna_Lfold(), vrna_Lfoldz(), #VRNA_OPTION_WINDOW, vrna_md_t.max_bp_span, vrna_md_t.window_size
Parameters
vcThe vrna_fold_compound_t with preallocated memory for the DP matrices
min_zThe minimal z-score for a predicted structure to appear in the output
fileThe output file handle where predictions are written to (maybe NULL)