RNAlib-2.4.5
Structure sampling from the ensemble

Detailed Description

+ Collaboration diagram for Structure sampling from 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 * vrna_pbacktrack5 (vrna_fold_compound_t *vc, int length)
 Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability. More...
 
char * vrna_pbacktrack (vrna_fold_compound_t *vc)
 Sample a secondary structure (consensus structure) from the Boltzmann ensemble according its probability. More...
 
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...
 

Function Documentation

◆ vrna_pbacktrack5()

char * vrna_pbacktrack5 ( vrna_fold_compound_t vc,
int  length 
)

#include <ViennaRNA/boltzmann_sampling.h>

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

Precondition
Unique multiloop decomposition has to be active upon creation of vc with vrna_fold_compound() or similar. This can be done easily by passing vrna_fold_compound() a model details parameter with vrna_md_t.uniq_ML = 1.
vrna_pf() has to be called first to fill the partition function matrices
Parameters
vcThe fold compound data structure
lengthThe length of the subsequence to consider (starting with 5' end)
Returns
A sampled secondary structure in dot-bracket notation (or NULL on error)
SWIG Wrapper Notes:
This function is attached as overloaded method pbacktrack() to objects of type fold_compound

◆ vrna_pbacktrack()

char * vrna_pbacktrack ( vrna_fold_compound_t vc)

#include <ViennaRNA/boltzmann_sampling.h>

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

Precondition
Unique multiloop decomposition has to be active upon creation of vc with vrna_fold_compound() or similar. This can be done easily by passing vrna_fold_compound() a model details parameter with vrna_md_t.uniq_ML = 1.
vrna_pf() has to be called first to fill the partition function matrices
Note
This function is polymorphic. It accepts vrna_fold_compound_t of type VRNA_FC_TYPE_SINGLE, and VRNA_FC_TYPE_COMPARATIVE.
The function will automagically detect cicular RNAs based on the model_details in exp_params as provided via the vrna_fold_compound_t
Parameters
vcThe fold compound data structure
Returns
A sampled secondary structure in dot-bracket notation (or NULL on error)
SWIG Wrapper Notes:
This function is attached as overloaded method pbacktrack() to objects of type fold_compound that accepts an optional length argument. Hence, it serves as a replacement for vrna_pbacktrack().

◆ pbacktrack()

char* pbacktrack ( char *  sequence)

#include <ViennaRNA/part_func.h>

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

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

◆ pbacktrack_circ()

char* pbacktrack_circ ( char *  sequence)

#include <ViennaRNA/part_func.h>

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
Deprecated:
Use vrna_pbacktrack() instead.
Parameters
sequenceThe RNA sequence
Returns
A sampled secondary structure in dot-bracket notation

Variable Documentation

◆ st_back

int st_back

#include <ViennaRNA/part_func.h>

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

Deprecated:
set the uniq_ML flag in vrna_md_t before passing it to vrna_fold_compound().
See also
pbacktrack(), pbacktrack_circ