Minimum Free Energy (MFE) algorithms

Overview

// typedefs

typedef void () vrna_mfe_window_callback (
    int start,
    int end,
    const char *structure,
    float en,
    void *data
    )

// global functions

float vrna_mfe (
    vrna_fold_compound_t* vc,
    char* structure
    )

Detailed Documentation

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.

Notes on Callback Functions This function will be called for each hit in a sliding window MFE prediction.

Parameters:

start provides the first position of the hit (1-based, relative to entire sequence/alignment)
end provides the last position of the hit (1-based, relative to the entire sequence/alignment)
structure provides the (sub)structure in dot-bracket notation
en is the free energy of the structure hit in kcal/mol
data is some arbitrary data pointer passed through by the function executing the callback

See also:

vrna_mfe_window()

Global Functions

float vrna_mfe (
    vrna_fold_compound_t* vc,
    char* structure
    )
Compute minimum free energy and an appropriate secondary structure of an RNA sequence, or RNA sequence alignment.

Depending on the type of the provided vrna_fold_compound_t , this function predicts the MFE for a single sequence, or a corresponding averaged MFE for a sequence alignment. If backtracking is activated, it also constructs the corresponding secondary structure, or consensus structure. Therefore, the second parameter, structure , has to point to an allocated block of memory with a size of at least \(\mathrm{strlen}(\mathrm{sequence})+1\) to store the backtracked MFE structure. (For consensus structures, this is the length of the alignment + 1. If NULL is passed, no backtracking will be performed.

SWIG Wrapper Notes This function is attached as method mfe() to objects of type fold_compound

Parameters:

vc fold compound
structure A pointer to the character array where the secondary structure in dot-bracket notation will be written to (Maybe NULL)

Returns:

the minimum free energy (MFE) in kcal/mol

Note

This function is polymorphic. It accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE , and VRNA_FC_TYPE_COMPARATIVE .