[Strategy Market] G and C bases in GC pairs

Strategy Market Strategy Market - Single State
1

I’d like to submit a strategy:

Rank designs based on the percentage of G and C bases that are part of GC pairs as a fraction of total G and C pairs.

That is: score = (200 * number of GC pairs) / (total G bases + total C bases)

So a design where all Gs and Cs are part of GC pairs would score 100, and a design where all Gs and Cs were either unpaired or part of GU pairs would score 0.

If possible, I’d like to exclude from the calculation G and C bases that are locked, such as in aptamer rings that are fixed for a given lab.

2

Slight nit: what if there are no Gs or Cs? Divide by zero error, but should probably score as 0 (cub scout design).

3

You’re right - that is a possibility. Since cub scout designs are known to do badly in synthesis, I agree with your suggestion that such designs should score 0 rather than crash the scoring algorithm.

I would hope all of the strategy market algorithms are implemented with exception handling, but I don’t know if that’s actually the case. Thanks for pointing out my oversight.