MFE Consensus Structures for Sequence Alignment(s)

Overview

// global functions

float vrna_alifold (
    const char** sequences,
    char* structure
    )

float vrna_circalifold (
    const char** sequences,
    char* structure
    )

float alifold (
    const char** strings,
    char* structure
    )

float circalifold (
    const char** strings,
    char* structure
    )

void free_alifold_arrays (void)

Detailed Documentation

Global Functions

float vrna_alifold (
    const char** sequences,
    char* structure
    )
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for an RNA sequence alignment using a comparative method.

This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary structure for an RNA sequence alignment using default options. 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, e.g. suboptimal backtracking, etc.

Parameters:

sequences RNA sequence alignment
structure A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns:

the minimum free energy (MFE) in kcal/mol

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() , and the data structure vrna_fold_compound_t instead.

float vrna_circalifold (
    const char** sequences,
    char* structure
    )
Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure for a sequence alignment of circular RNAs using a comparative method.

This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary structure for an RNA sequence alignment using default options. 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, e.g. suboptimal backtracking, etc.

Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [7] for further details.

Parameters:

sequences Sequence alignment of circular RNAs
structure A pointer to the character array where the secondary structure in dot-bracket notation will be written to

Returns:

the minimum free energy (MFE) in kcal/mol

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() , and the data structure vrna_fold_compound_t instead.

float alifold (
    const char** strings,
    char* structure
    )
Compute MFE and according consensus structure of an alignment of sequences.

This function predicts the consensus structure for the aligned ‘sequences’ and returns the minimum free energy; the mfe structure in bracket notation is returned in ‘structure’.

Sufficient space must be allocated for ‘structure’ before calling alifold() .

Deprecated Usage of this function is discouraged! Use vrna_alifold() , or vrna_mfe() instead!

Parameters:

strings A pointer to a NULL terminated array of character arrays
structure A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE)

Returns:

The free energy score in kcal/mol

float circalifold (
    const char** strings,
    char* structure
    )
Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear.

Deprecated Usage of this function is discouraged! Use vrna_alicircfold(), and vrna_mfe() instead!

Parameters:

strings A pointer to a NULL terminated array of character arrays
structure A pointer to a character array that may contain a constraining consensus structure (will be overwritten by a consensus structure that exhibits the MFE)

Returns:

The free energy score in kcal/mol

See also:

vrna_alicircfold(), vrna_alifold() , vrna_mfe()

void free_alifold_arrays (void)
Free the memory occupied by MFE alifold functions.

Deprecated Usage of this function is discouraged! It only affects memory being free’d that was allocated by an old API function before. Release of memory occupied by the newly introduced vrna_fold_compound_t is handled by vrna_fold_compound_free()