Local MFE structure Prediction and Z-scores
RNA Secondary Structure Prediction » Predicting Locally stable structures of large sequences RNA Secondary Structure Prediction » | Computing Minimum Free Energy (MFE) Structures
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

  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.

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

  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'

Deprecated:
  Use vrna_mfe_window() instead!

float Lfoldz | ( | const char * | string,
|  | char * | structure,
|  | int | maxdist,
|  | int | zsc,
|  | double | min_z
| ) |  |

`#include <ViennaRNA/Lfold.h>`

Deprecated:
  Use vrna_mfe_window_zscore() instead!

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

  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.

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

  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)