RNAlib-2.2.0-RC3
+ Collaboration diagram for Partition Function and Base Pair Probabilities for Sequence Alignment(s):

Functions

float vrna_ali_pf_fold (vrna_fold_compound *vc, char *structure, plist **pl)
 Compute partition function and base pair probabilities for a sequence alignment. More...
 
float alipf_fold_par (const char **sequences, char *structure, plist **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular)
 
float alipf_fold (const char **sequences, char *structure, plist **pl)
 The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of pair_info structs. The list is terminated by the first entry with pi.i = 0. More...
 
float alipf_circ_fold (const char **sequences, char *structure, plist **pl)
 
FLT_OR_DBL * export_ali_bppm (void)
 Get a pointer to the base pair probability array. More...
 
void free_alipf_arrays (void)
 Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc. More...
 

Detailed Description

Function Documentation

float vrna_ali_pf_fold ( vrna_fold_compound vc,
char *  structure,
plist **  pl 
)

Compute partition function and base pair probabilities for a sequence alignment.

The partition function version of vrna_ali_fold() works in analogy to vrna_pf_fold(). Pair probabilities are returned via the 'pl' variable as a list of plist structs. The list is terminated by the first entry with pl.i = 0.

See also
vrna_ali_get_pair_info() for a replacement of pl with more detailed information
Parameters
vcThe vrna_fold_compound of type VRNA_VC_TYPE_ALIGNMENT
structureA pointer to a character array of length of the alignment (Maybe NULL)
plA pointer to a plist pointer where the pair probabilities are stored (Maybe NULL)
Returns
Gibbs free energy of the consensus fold space
float alipf_fold_par ( const char **  sequences,
char *  structure,
plist **  pl,
vrna_exp_param_t parameters,
int  calculate_bppm,
int  is_constrained,
int  is_circular 
)
Deprecated:
Use vrna_ali_pf_fold() instead
Parameters
sequences
structure
pl
parameters
calculate_bppm
is_constrained
is_circular
Returns
float alipf_fold ( const char **  sequences,
char *  structure,
plist **  pl 
)

The partition function version of alifold() works in analogy to pf_fold(). Pair probabilities and information about sequence covariations are returned via the 'pi' variable as a list of pair_info structs. The list is terminated by the first entry with pi.i = 0.

Deprecated:
Use vrna_ali_pf_fold() instead
Parameters
sequences
structure
pl
Returns
float alipf_circ_fold ( const char **  sequences,
char *  structure,
plist **  pl 
)
Deprecated:
Use vrna_ali_pf_fold() instead
Parameters
sequences
structure
pl
Returns
FLT_OR_DBL* export_ali_bppm ( void  )

Get a pointer to the base pair probability array.

Accessing the base pair probabilities for a pair (i,j) is achieved by

FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; 
Deprecated:
Usage of this function is discouraged! The new vrna_fold_compound allows direct access to the folding matrices, including the pair probabilities! The pair probability array returned here reflects the one of the latest call to vrna_ali_pf_fold(), or any of the old API calls for consensus structure partition function folding.
See also
vrna_fold_compound, vrna_get_fold_compound_ali(), and vrna_ali_pf_fold()
Returns
A pointer to the base pair probability array
void free_alipf_arrays ( void  )

Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.

Deprecated:
Usage of this function is discouraged! This function only free's memory allocated by old API function calls. Memory allocated by any of the new API calls (starting with vrna_) will be not affected!
See also
vrna_fold_compound, vrna_vrna_free_fold_compound()