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

Include dependency graph for alifold.h:

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

Functions

Variables

Detailed Description

Function Documentation