If you were able to quantify the dot plot into percentages you could design
scripts that try to remove the mismatches that cause the non-desired matches
after a solution has been found for the puzzle.
I think all you have to do is save the value computed for the dot and compare to any new value after the modification.
If the pair is supposed to form but hasn’t then you want new value>old.
If the pair has formed but shouldn’t you want new valuet say.
That’s what I want. The formula for computing each dot value. Anyone know where I can find it?
The Free Energy of a shape determines its relative abundance in solution. I run RNAsubopt to determine the possible foldings for a given RNA sequence, then compute a weight for each shape as follows:
var feBase = 5.27;
function feToWeight(fe) { return Math.pow(feBase,-fe); }
The exact value of feBase depends on the target temperature.
I then look at all predicted shapes that have a given bond formed and sum those weights, then divide by the total weights for all predicted shapes. That gives a probability of the given bond forming. Repeat for all possible bonds.
I don’t know if any of the newer tools will do that for you. I started scripting before there was much assistance for that sort of thing in the libraries and have not been scripting much in the past few months.