RNAlib-2.1.8
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
.
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.

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:
sequenceThe 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

\pre    #st_back has to be set to 1 before calling pf_fold() or pf_fold_par()
\pre    pf_fold_par() or pf_circ_fold() have to be called first to fill the partition function matrices

\param  sequence  The RNA sequence
\return           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