RNAlib-2.2.0-RC3

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

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Functions

float vrna_ali_fold (vrna_fold_compound *vc, char *structure)
 Compute MFE and according consensus structure of an alignment of sequences. 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 vrna_ali_pf_fold (vrna_fold_compound *vc, char *structure, plist **pl)
 Compute partition function and base pair probabilities for a sequence alignment. More...
 
pair_infovrna_ali_get_pair_info (vrna_fold_compound *vc, const char *structure, double threshold)
 Retrieve an array of pair_info structures from precomputed pair probabilities. 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...
 
char * vrna_ali_pbacktrack (vrna_fold_compound *vc, double *prob)
 Sample a consensus secondary structure from the Boltzmann ensemble according its probability
. 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, int **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

Function Documentation

pair_info* vrna_ali_get_pair_info ( vrna_fold_compound vc,
const char *  structure,
double  threshold 
)

Retrieve an array of pair_info structures from precomputed pair probabilities.

This array of structures contains information about positionwise pair probabilies, base pair entropy and more

See also
pair_info, and vrna_ali_pf_fold()
Parameters
vcThe vrna_fold_compound of type VRNA_VC_TYPE_ALIGNMENT with precomputed partition function matrices
structureAn optional structure in dot-bracket notation (Maybe NULL)
thresholdDo not include results with pair probabilities below threshold
Returns
The pair_info array