RNAlib-2.2.7
+ Collaboration diagram for MFE Consensus Structures for Sequence Alignment(s):

Functions

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

#include <ViennaRNA/alifold.h>

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.

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.
See also
vrna_circalifold(), vrna_mfe(), vrna_fold_compound(), vrna_fold_compound_t
Parameters
sequencesRNA sequence alignment
structureA 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
float vrna_circalifold ( const char **  ssequences,
char *  structure 
)

#include <ViennaRNA/alifold.h>

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 [6] for further details.

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.
See also
vrna_alifold(), vrna_mfe(), vrna_fold_compound(), vrna_fold_compound_t
Parameters
sequencesSequence alignment of circular RNAs
structureA 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
float alifold ( const char **  strings,
char *  structure 
)

#include <ViennaRNA/alifold.h>

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!
See also
vrna_alifold(), vrna_mfe()
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 
)

#include <ViennaRNA/alifold.h>

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!
See also
vrna_alicircfold(), vrna_alifold(), vrna_mfe()
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  )

#include <ViennaRNA/alifold.h>

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_vrna_fold_compound_free()
See also
vrna_vrna_fold_compound_free()