RNA sequence design. More…
// global variables char* symbolset float final_cost int give_up int inv_verbose // global functions float inverse_fold ( char* start, const char* target ) float inverse_pf_fold ( char* start, const char* target )
char* symbolset
float final_cost
int give_up
int inv_verbose
float inverse_fold ( char* start, const char* target )
This function searches for a sequence with minimum free energy structure provided in the parameter ‘target’, starting with sequence ‘start’. It returns 0 if the search was successful, otherwise a structure distance in terms of the energy difference between the search result and the actual target ‘target’ is returned. The found sequence is returned in ‘start’. If give_up is set to 1, the function will return as soon as it is clear that the search will be unsuccessful, this speeds up the algorithm if you are only interested in exact solutions.
Parameters:
start | The start sequence |
target | The target secondary structure in dot-bracket notation |
Returns:
The distance to the target in case a search was unsuccessful, 0 otherwise
float inverse_pf_fold ( char* start, const char* target )
This function searches for a sequence with maximum probability to fold into the provided structure ‘target’ using the partition function algorithm. It returns \(-kT \cdot \log(p)\) where \(p\) is the frequency of ‘target’ in the ensemble of possible structures. This is usually much slower than inverse_fold() .
Parameters:
start | The start sequence |
target | The target secondary structure in dot-bracket notation |
Returns:
The distance to the target in case a search was unsuccessful, 0 otherwise