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
Find sequence that maximizes probability of a predefined structure.
This function searches for a sequence with maximum probability to fold into the provided structure 'target' using the partition function algorithm. It returns where 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