RNAlib-2.2.7

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 $Q$ (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 $Q$ (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_DBLexport_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