MFE Consensus Structures for Sequence Alignment(s)

Collaboration diagram for MFE Consensus Structures for Sequence Alignment(s):

Functions
float	alifold (const char **strings, char *structure)
	Compute MFE and according consensus structure of an alignment of sequences. More...
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. More...
void	free_alifold_arrays (void)
	Free the memory occupied by MFE alifold functions.

Detailed Description

Function Documentation

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().

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.

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