alifold.h File Reference
RNA Secondary Structure Prediction » Predicting Consensus Structures from Alignment(s)

compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments More...

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## 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 | vrna_pf_alifold (const char **strings, char *structure, vrna_plist_t **pl)
| Compute Partition function (and base pair probabilities) for an RNA sequence alignment using a comparative method. More...
float | vrna_pf_circalifold (const char **sequences, char *structure, vrna_plist_t **pl)
| Compute Partition function (and base pair probabilities) for an alignment of circular RNA sequences 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...
float | energy_of_alistruct (const char **sequences, const char *structure, int n_seq, float *energy)
| Calculate the free energy of a consensus structure given a set of aligned sequences. More...
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...
char * | alipbacktrack (double *prob)
| Sample a consensus secondary structure from the Boltzmann ensemble according its probability. More...
int | get_alipf_arrays (short ***S_p, short ***S5_p, short ***S3_p, unsigned short ***a2s_p, char ***Ss_p, FLT_OR_DBL **qb_p, FLT_OR_DBL **qm_p, FLT_OR_DBL **q1k_p, FLT_OR_DBL **qln_p, short **pscore)
| Get pointers to (almost) all relavant arrays used in alifold's partition function computation. More...
void | update_alifold_params (void)
| Update the energy parameters for alifold function. More...

## Variables

double | cv_fact
| This variable controls the weight of the covariance term in the energy function of alignment folding algorithms. More...
double | nc_fact
| This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms. More...

## Detailed Description

compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments