alifold.h File Reference

Functions for comparative structure prediction using RNA sequence alignments. More...

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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...

Detailed Description

Functions for comparative structure prediction using RNA sequence alignments.

Function Documentation

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.

Deprecated:

Usage of this function is discouraged! Use vrna_eval_structure(), and vrna_eval_covar_structure() instead!

Parameters

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)

Returns

free energy in kcal/mol

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

Deprecated:

Usage of this function is discouraged! The new API uses vrna_fold_compound_t to lump all folding related necessities together, including the energy parameters. Use vrna_update_fold_params() to update the energy parameters within a vrna_fold_compound_t.

Variable Documentation

double cv_fact

This variable controls the weight of the covariance term in the energy function of alignment folding algorithms.

Deprecated:

See vrna_md_t.cv_fact, and vrna_mfe() to avoid using global variables

Default is 1.

double nc_fact

This variable controls the magnitude of the penalty for non-compatible sequences in the covariance term of alignment folding algorithms.

Deprecated:

See vrna_md_t.nc_fact, and vrna_mfe() to avoid using global variables

Default is 1.