Stochastic backtracking in the Ensemble
[Enumerating Suboptimal Structures]

Collaboration diagram for Stochastic backtracking in the Ensemble:

Modules
	Stochastic Backtracking of Consensus Structures from Sequence Alignment(s)
	Stochastic Backtracking of Structures from Distance Based Partitioning
	Contains functions related to stochastic backtracking from a specified distance class.
Functions
char *	pbacktrack (char *sequence)
	Sample a secondary structure from the Boltzmann ensemble according its probability .
char *	pbacktrack_circ (char *sequence)
	Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability.
Variables
int	st_back
	Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.

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Function Documentation

char* pbacktrack

(

char *

sequence

)

Sample a secondary structure from the Boltzmann ensemble according its probability
.

Precondition:

pf_fold_par() or pf_fold() have to be called first to fill the partition function matrices

Parameters:

sequence

The RNA sequence

Returns:

A sampled secondary structure in dot-bracket notation

char* pbacktrack_circ

(

char *

sequence

)

Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability.

This function does the same as pbacktrack() but assumes the RNA molecule to be circular

Precondition:

pf_fold_par() or pf_fold_circ() have to be called first to fill the partition function matrices

Parameters:

sequence

The RNA sequence

Returns:

A sampled secondary structure in dot-bracket notation

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Variable Documentation

int st_back

Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking.

Set this variable to 1 prior to a call of pf_fold() to ensure that all matrices needed for stochastic backtracking are filled in the forward recursions

See also:

pbacktrack(), pbacktrack_circ