RNAlib-2.2.7
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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... | |
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.
vc | The fold compound data structure |
length | The length of the subsequence to consider (starting with 5' end) |
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.
vc | The fold compound data structure |
length | The length of the subsequence to consider (starting with 5' end) |
char* pbacktrack | ( | char * | sequence | ) |
#include <ViennaRNA/part_func.h>
Sample a secondary structure from the Boltzmann ensemble according its probability.
sequence | The RNA sequence |
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
sequence | The RNA sequence |
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