Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints. More...

Detailed Description

Incorporate SHAPE reactivity structure probing data into the folding recursions by means of soft constraints.

Details for our implementation to incorporate SHAPE reactivity data to guide secondary structure prediction can be found in [16]

Collaboration diagram for SHAPE Reactivity Data:

Files
file	SHAPE.h
	This module provides function to incorporate SHAPE reactivity data into the folding recursions by means of soft constraints.

Functions
int	vrna_sc_add_SHAPE_deigan (vrna_fold_compound_t vc, const double reactivities, double m, double b, unsigned int options)
	Add SHAPE reactivity data as soft constraints (Deigan et al. method) More...

int	vrna_sc_add_SHAPE_deigan_ali (vrna_fold_compound_t vc, const char shape_files, const int shape_file_association, double m, double b, unsigned int options)
	Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method) More...

int	vrna_sc_add_SHAPE_zarringhalam (vrna_fold_compound_t vc, const double reactivities, double b, double default_value, const char *shape_conversion, unsigned int options)
	Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method) More...

int	vrna_sc_SHAPE_to_pr (const char shape_conversion, double values, int length, double default_value)
	Convert SHAPE reactivity values to probabilities for being unpaired. More...

Function Documentation

int vrna_sc_add_SHAPE_deigan	(	vrna_fold_compound_t *	vc,
		const double *	reactivities,
		double	m,
		double	b,
		unsigned int	options
	)

#include <ViennaRNA/constraints/SHAPE.h>

Add SHAPE reactivity data as soft constraints (Deigan et al. method)

This approach of SHAPE directed RNA folding uses the simple linear ansatz

$\Delta G_{\text{SHAPE}}(i) = m \ln(\text{SHAPE reactivity}(i)+1)+ b$

to convert SHAPE reactivity values to pseudo energies whenever a nucleotide $ i $ contributes to a stacked pair. A positive slope $ m $ penalizes high reactivities in paired regions, while a negative intercept $ b $ results in a confirmatory ``bonus'' free energy for correctly predicted base pairs. Since the energy evaluation of a base pair stack involves two pairs, the pseudo energies are added for all four contributing nucleotides. Consequently, the energy term is applied twice for pairs inside a helix and only once for pairs adjacent to other structures. For all other loop types the energy model remains unchanged even when the experimental data highly disagrees with a certain motif.

See also: For further details, we refer to [6].; vrna_sc_remove(), vrna_sc_add_SHAPE_zarringhalam(), vrna_sc_minimize_pertubation()

Parameters

vc	The vrna_fold_compound_t the soft constraints are associated with
reactivities	A vector of normalized SHAPE reactivities
m	The slope of the conversion function
b	The intercept of the conversion function
options	The options flag indicating how/where to store the soft constraints

Returns: 1 on successful extraction of the method, 0 on errors

SWIG Wrapper Notes:: This function is attached as method sc_add_SHAPE_deigan() to objects of type fold_compound

int vrna_sc_add_SHAPE_deigan_ali	(	vrna_fold_compound_t *	vc,
		const char **	shape_files,
		const int *	shape_file_association,
		double	m,
		double	b,
		unsigned int	options
	)

#include <ViennaRNA/constraints/SHAPE.h>

Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method)

Parameters

vc	The vrna_fold_compound_t the soft constraints are associated with
shape_files	A set of filenames that contain normalized SHAPE reactivity data
shape_file_association	An array of integers that associate the files with sequences in the alignment
m	The slope of the conversion function
b	The intercept of the conversion function
options	The options flag indicating how/where to store the soft constraints

Returns: 1 on successful extraction of the method, 0 on errors

SWIG Wrapper Notes:: This function is attached as method sc_add_SHAPE_deigan_ali() to objects of type fold_compound

int vrna_sc_add_SHAPE_zarringhalam	(	vrna_fold_compound_t *	vc,
		const double *	reactivities,
		double	b,
		double	default_value,
		const char *	shape_conversion,
		unsigned int	options
	)

#include <ViennaRNA/constraints/SHAPE.h>

Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method)

This method first converts the observed SHAPE reactivity of nucleotide $ i $ into a probability $ q_i $ that position $ i $ is unpaired by means of a non-linear map. Then pseudo-energies of the form

$\Delta G_{\text{SHAPE}}(x,i) = \beta\ |x_i - q_i|$

are computed, where $ x_i=0 $ if position $ i $ is unpaired and $ x_i=1 $ if $ i $ is paired in a given secondary structure. The parameter $\beta$ serves as scaling factor. The magnitude of discrepancy between prediction and experimental observation is represented by $ |x_i - q_i| $ .

See also: For further details, we refer to [25]; vrna_sc_remove(), vrna_sc_add_SHAPE_deigan(), vrna_sc_minimize_pertubation()

Parameters

vc	The vrna_fold_compound_t the soft constraints are associated with
reactivities	A vector of normalized SHAPE reactivities
b	The scaling factor $\beta$ of the conversion function
default_value	The default value for a nucleotide where reactivity data is missing for
shape_conversion	A flag that specifies how to convert reactivities to probabilities
options	The options flag indicating how/where to store the soft constraints

Returns: 1 on successful extraction of the method, 0 on errors

SWIG Wrapper Notes:: This function is attached as method sc_add_SHAPE_zarringhalam() to objects of type fold_compound

int vrna_sc_SHAPE_to_pr	(	const char *	shape_conversion,
		double *	values,
		int	length,
		double	default_value
	)

#include <ViennaRNA/constraints/SHAPE.h>

Convert SHAPE reactivity values to probabilities for being unpaired.

This function parses the informations from a given file and stores the result in the preallocated string sequence and the FLT_OR_DBL array values.

See also: vrna_file_SHAPE_read()

Parameters

shape_conversion	String definining the method used for the conversion process
values	Pointer to an array of SHAPE reactivities
length	Length of the array of SHAPE reactivities
default_value	Result used for position with invalid/missing reactivity values

Detailed Description

Files

Functions

Function Documentation