RNAlib-2.2.0RC0
+ Collaboration diagram for MFE Consensus Structures for Sequence Alignment(s):

Functions

float vrna_ali_fold (vrna_fold_compound *vc, char *structure)
 Compute MFE and according consensus structure of an alignment of sequences. More...
 
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. More...
 

Detailed Description

Function Documentation

float vrna_ali_fold ( vrna_fold_compound vc,
char *  structure 
)

Compute MFE and according consensus structure of an alignment of sequences.

This function predicts the consensus structure for the aligned stored in vc and returns the minimum free energy; the mfe structure in bracket notation is returned in 'structure'.

Note
vc has to be of type VRNA_VC_TYPE_ALIGNMENT.
Sufficient space must be allocated for 'structure' before calling vrna_ali_fold(). Passing NULL to the 'structure' or setting model_detailsT.backtrack to 0 turns of backtracing an no structure will be returned.
See also
vrna_get_fold_compound_ali()
Parameters
vcThe fold compound structure of type VRNA_VC_TYPE_ALIGNMENT
structureA pointer to a character array that will be overwritten by a consensus structure that exhibits the MFE. (Maybe NULL)
Returns
The free energy score in kcal/mol
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_ali_fold() instead
See also
vrna_ali_fold()
Parameters
stringsA pointer to a NULL terminated array of character arrays
structureA 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_ali_fold() instead
See also
vrna_ali_fold()
Parameters
stringsA pointer to a NULL terminated array of character arrays
structureA 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
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 is handled by vrna_vrna_free_fold_compound()
See also
vrna_vrna_free_fold_compound()