mfe_window.h File Reference

Compute local Minimum Free Energy (MFE) using a sliding window approach and backtrace corresponding secondary structures. More...

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Typedefs
typedef void(	vrna_mfe_window_callback) (int start, int end, const char *structure, float en, void *data)
	The default callback for sliding window MFE structure predictions. More...

Functions
Basic local (sliding window) MFE prediction interface
float	vrna_mfe_window (vrna_fold_compound_t *vc, FILE *file)
	Local MFE prediction using a sliding window approach. More...
float	vrna_mfe_window_cb (vrna_fold_compound_t *vc, vrna_mfe_window_callback *cb, void *data)
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_mfe_window_zscore_cb (vrna_fold_compound_t *vc, double min_z, vrna_mfe_window_zscore_callback *cb, void *data)
Simplified local MFE prediction using sequence(s) or multiple sequence alignment(s)
float	vrna_Lfold (const char *string, int window_size, FILE *file)
	Local MFE prediction using a sliding window approach (simplified interface) More...
float	vrna_Lfold_cb (const char *string, int window_size, vrna_mfe_window_callback *cb, void *data)
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	vrna_Lfoldz_cb (const char *string, int window_size, double min_z, vrna_mfe_window_zscore_callback *cb, void *data)
float	vrna_aliLfold (const char **alignment, int maxdist, FILE *fp)
float	vrna_aliLfold_cb (const char **alignment, int maxdist, vrna_mfe_window_callback *cb, void *data)

Detailed Description

Compute local Minimum Free Energy (MFE) using a sliding window approach and backtrace corresponding secondary structures.

, This file includes the interface to all functions related to predicting locally stable secondary structures.