Stochastic backtracking in the Ensemble

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 . More...
char *	pbacktrack_circ (char *sequence)
	Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability. More...

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

Detailed Description

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

st_back has to be set to 1 before calling pf_fold() or pf_fold_par()

pf_fold_par() or pf_circ_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

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