Stochastic Backtracking of Structures from Distance Based Partitioning

Overview

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

// global functions

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

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

Detailed Documentation

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

Global 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.

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.

Parameters:

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

Returns:

A sampled secondary structure in dot-bracket notation

Pre-Condition

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()

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.

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

Parameters:

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

Returns:

A sampled secondary structure in dot-bracket notation

Note

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

Pre-Condition

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