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RNAlib-2.4.17
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Functions for comparative structure prediction using RNA sequence alignments. More...
Include dependency graph for alifold.h:Go to the source code of this file.
Functions | |
| 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... | |
| void | update_alifold_params (void) |
| Update the energy parameters for alifold function. 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 | alipf_fold_par (const char **sequences, char *structure, vrna_ep_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_ep_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_ep_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... | |
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... | |
Functions for comparative structure prediction using RNA sequence alignments.
| float energy_of_alistruct | ( | const char ** | sequences, |
| const char * | structure, | ||
| int | n_seq, | ||
| float * | energy | ||
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Calculate the free energy of a consensus structure given a set of aligned sequences.
| sequences | The NULL terminated array of sequences |
| structure | The consensus structure |
| n_seq | The number of sequences in the alignment |
| energy | A pointer to an array of at least two floats that will hold the free energies (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term) |
| void update_alifold_params | ( | void | ) |
Update the energy parameters for alifold function.
Call this to recalculate the pair matrix and energy parameters after a change in folding parameters like temperature
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extern |
This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.
Default is 1.
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extern |
This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms.
Default is 1.