Stochastic Backtracking of Structures from Distance Based Partitioning

Contains functions related to stochastic backtracking from a specified distance class. More...

Detailed Description

Contains functions related to stochastic backtracking from a specified distance class.

Collaboration diagram for Stochastic Backtracking of Structures from Distance Based Partitioning:

Functions
char *	vrna_pbacktrack_TwoD (vrna_fold_compound_t *vc, int d1, int d2)
	Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability. More...
char *	vrna_pbacktrack5_TwoD (vrna_fold_compound_t *vc, int d1, int d2, unsigned int length)
	Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability. More...

Function Documentation

char* vrna_pbacktrack_TwoD	(	vrna_fold_compound_t *	vc,
		int	d1,
		int	d2
	)

#include <ViennaRNA/2Dpfold.h>

Sample secondary structure representatives from a set of distance classes according to their Boltzmann probability.

If the argument 'd1' is set to '-1', the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.

Precondition

The argument 'vars' must contain precalculated partition function matrices, i.e. a call to vrna_pf_TwoD() preceding this function is mandatory!

See also

vrna_pf_TwoD()

Parameters

[in,out]	vc	The vrna_fold_compound_t datastructure containing all necessary folding attributes and matrices
[in]	d1	The distance to reference1 (may be -1)
[in]	d2	The distance to reference2

Returns

A sampled secondary structure in dot-bracket notation

char* vrna_pbacktrack5_TwoD	(	vrna_fold_compound_t *	vc,
		int	d1,
		int	d2,
		unsigned int	length
	)

#include <ViennaRNA/2Dpfold.h>

Sample secondary structure representatives with a specified length from a set of distance classes according to their Boltzmann probability.

This function does essentially the same as vrna_pbacktrack_TwoD() with the only difference that partial structures, i.e. structures beginning from the 5' end with a specified length of the sequence, are backtracked

Note

This function does not work (since it makes no sense) for circular RNA sequences!

Precondition

The argument 'vars' must contain precalculated partition function matrices, i.e. a call to vrna_pf_TwoD() preceding this function is mandatory!

See also

vrna_pbacktrack_TwoD(), vrna_pf_TwoD()

Parameters

[in,out]	vc	The vrna_fold_compound_t datastructure containing all necessary folding attributes and matrices
[in]	d1	The distance to reference1 (may be -1)
[in]	d2	The distance to reference2
[in]	length	The length of the structure beginning from the 5' end

Returns

A sampled secondary structure in dot-bracket notation