Comparative structure prediction

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

Collaboration diagram for Comparative structure prediction:

Modules
	MFE Consensus Structures for Sequence Alignment(s)
	Partition Function and Base Pair Probabilities for Sequence Alignment(s)
	Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)
	Local MFE Consensus Structure Prediction for Sequence Alignments

Files
file	alifold.h
	Functions for comparative structure prediction using RNA sequence alignments.

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...
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...
void	update_alifold_params (void)
	Update the energy parameters for alifold function. More...
float **	get_ribosum (const char **Alseq, int n_seq, int length)
	Retrieve a RiboSum Scoring Matrix for a given Alignment.

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

Consensus structures can be predicted by a modified version of the fold() algorithm that takes a set of aligned sequences instead of a single sequence. The energy function consists of the mean energy averaged over the sequences, plus a covariance term that favors pairs with consistent and compensatory mutations and penalizes pairs that cannot be formed by all structures. For details see [9] and [2].

Function Documentation

energy_of_alistruct()

float energy_of_alistruct	(	const char **	sequences,
		const char *	structure,
		int	n_seq,
		float *	energy
	)

#include <ViennaRNA/alifold.h>

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

get_alipf_arrays()

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
	)

#include <ViennaRNA/alifold.h>

Get pointers to (almost) all relavant arrays used in alifold's partition function computation.

Note

To obtain meaningful pointers, call alipf_fold first!

See also

pf_alifold(), alipf_circ_fold()

Deprecated:

It is discouraged to use this function! The new vrna_fold_compound_t allows direct access to all necessary consensus structure prediction related variables!

See also

vrna_fold_compound_t, vrna_fold_compound_comparative(), vrna_pf()

Parameters

S_p	A pointer to the 'S' array (integer representation of nucleotides)
S5_p	A pointer to the 'S5' array
S3_p	A pointer to the 'S3' array
a2s_p	A pointer to the alignment-column to sequence position mapping array
Ss_p	A pointer to the 'Ss' array
qb_p	A pointer to the QB matrix
qm_p	A pointer to the QM matrix
q1k_p	A pointer to the 5' slice of the Q matrix ( )
qln_p	A pointer to the 3' slice of the Q matrix ( )
pscore	A pointer to the start of a pscore list

Returns

Non Zero if everything went fine, 0 otherwise

update_alifold_params()

void update_alifold_params

(

void

)

#include <ViennaRNA/alifold.h>

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

cv_fact

double cv_fact

#include <ViennaRNA/alifold.h>

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.

nc_fact

double nc_fact

#include <ViennaRNA/alifold.h>

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.