RNAlib-2.2.0RC0
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compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments More...
Go to the source code of this file.
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_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. More... | |
float | alipf_fold_par (const char **sequences, char *structure, plist **pl, pf_paramT *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... | |
compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
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
vc | The #vrna_old_compound of type VRNA_VC_TYPE_ALIGNMENT with precomputed partition function matrices |
structure | An optional structure in dot-bracket notation (Maybe NULL) |
threshold | Do not include results with pair probabilities below threshold |