RNAlib-2.1.9
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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 | |
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. | |
int | get_mpi (char *Alseq[], int n_seq, int length, int *mini) |
Get the mean pairwise identity in steps from ?to?(ident) More... | |
float ** | readribosum (char *name) |
Read a ribosum or other user-defined scoring matrix. | |
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 | encode_ali_sequence (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ) |
Get arrays with encoded sequence of the alignment. More... | |
void | alloc_sequence_arrays (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ) |
Allocate memory for sequence array used to deal with aligned sequences. More... | |
void | free_sequence_arrays (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss) |
Free the memory of the sequence arrays used to deal with aligned sequences. 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) |
double * | export_ali_bppm (void) |
Get a pointer to the base pair probability array. 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, double **qb_p, double **qm_p, double **q1k_p, double **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... | |
compute various properties (consensus MFE structures, partition function, Boltzmann distributed stochastic samples, ...) for RNA sequence alignments
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