Contains functions related to stochastic backtracking from a specified distance class. More…
// global functions char* vrna_pbacktrack_TwoD ( vrna_fold_compound_t* vc, int d1, int d2 ) char* vrna_pbacktrack5_TwoD ( vrna_fold_compound_t* vc, int d1, int d2, unsigned int length )
char* vrna_pbacktrack_TwoD ( vrna_fold_compound_t* vc, int d1, int d2 )
If the argument ‘d1’ is set to ‘-1’, the structure will be backtracked in the distance class where all structures exceeding the maximum basepair distance to either of the references reside.
Parameters:
vc | The vrna_fold_compound_t datastructure containing all necessary folding attributes and matrices |
d1 | The distance to reference1 (may be -1) |
d2 | The distance to reference2 |
Returns:
A sampled secondary structure in dot-bracket notation
Pre-Condition
The argument ‘vars’ must contain precalculated partition function matrices, i.e. a call to vrna_pf_TwoD() preceding this function is mandatory!
See also:
char* vrna_pbacktrack5_TwoD ( vrna_fold_compound_t* vc, int d1, int d2, unsigned int length )
This function does essentially the same as vrna_pbacktrack_TwoD() with the only difference that partial structures, i.e. structures beginning from the 5’ end with a specified length of the sequence, are backtracked
Parameters:
vc | The vrna_fold_compound_t datastructure containing all necessary folding attributes and matrices |
d1 | The distance to reference1 (may be -1) |
d2 | The distance to reference2 |
length | The length of the structure beginning from the 5’ end |
Returns:
A sampled secondary structure in dot-bracket notation
Note
This function does not work (since it makes no sense) for circular RNA sequences!
Pre-Condition
The argument ‘vars’ must contain precalculated partition function matrices, i.e. a call to vrna_pf_TwoD() preceding this function is mandatory!
See also: