RNAlib-2.1.9

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

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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...
 

Detailed Description

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

Function Documentation

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