RNAlib-2.2.7
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Functions | |
float | vrna_pf_alifold (const char **strings, char *structure, vrna_plist_t **pl) |
Compute Partition function ![]() | |
float | vrna_pf_circalifold (const char **sequences, char *structure, vrna_plist_t **pl) |
Compute Partition function ![]() | |
float | alipf_fold_par (const char **sequences, char *structure, vrna_plist_t **pl, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained, int is_circular) |
float | alipf_fold (const char **sequences, char *structure, vrna_plist_t **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 vrna_pinfo_t structs. The list is terminated by the first entry with pi.i = 0. More... | |
float | alipf_circ_fold (const char **sequences, char *structure, vrna_plist_t **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... | |
float vrna_pf_alifold | ( | const char ** | strings, |
char * | structure, | ||
vrna_plist_t ** | pl | ||
) |
#include <ViennaRNA/alifold.h>
Compute Partition function (and base pair probabilities) for an RNA sequence alignment using a comparative method.
This simplified interface to vrna_pf() computes the partition function and, if required, base pair probabilities 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.
sequences | RNA sequence alignment |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_plist_t to store pairing probabilities (Maybe NULL) |
float vrna_pf_circalifold | ( | const char ** | sequences, |
char * | structure, | ||
vrna_plist_t ** | pl | ||
) |
#include <ViennaRNA/alifold.h>
Compute Partition function (and base pair probabilities) for an alignment of circular RNA sequences using a comparative method.
This simplified interface to vrna_pf() computes the partition function and, if required, base pair probabilities 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.
Folding of circular RNA sequences is handled as a post-processing step of the forward recursions. See [6] for further details.
sequences | Sequence alignment of circular RNAs |
structure | A pointer to the character array where position-wise pairing propensity will be stored. (Maybe NULL) |
pl | A pointer to a list of vrna_plist_t to store pairing probabilities (Maybe NULL) |
float alipf_fold_par | ( | const char ** | sequences, |
char * | structure, | ||
vrna_plist_t ** | pl, | ||
vrna_exp_param_t * | parameters, | ||
int | calculate_bppm, | ||
int | is_constrained, | ||
int | is_circular | ||
) |
#include <ViennaRNA/alifold.h>
sequences | |
structure | |
pl | |
parameters | |
calculate_bppm | |
is_constrained | |
is_circular |
float alipf_fold | ( | const char ** | sequences, |
char * | structure, | ||
vrna_plist_t ** | pl | ||
) |
#include <ViennaRNA/alifold.h>
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 vrna_pinfo_t structs. The list is terminated by the first entry with pi.i = 0.
sequences | |
structure | |
pl |
float alipf_circ_fold | ( | const char ** | sequences, |
char * | structure, | ||
vrna_plist_t ** | pl | ||
) |
#include <ViennaRNA/alifold.h>
sequences | |
structure | |
pl |
FLT_OR_DBL* export_ali_bppm | ( | void | ) |
#include <ViennaRNA/alifold.h>
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];
void free_alipf_arrays | ( | void | ) |
#include <ViennaRNA/alifold.h>
Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.