I would like to ad a strategy that says - no more than 2 blue nucleotides in tetraloops - that includes blue nucleotides in the closing basepair in the tetraloop too.
I would like to penalize with -1 for each extra blue nucleotide here.
This strategy is based on the Eterna tetraloop reference table and robot tendency to put in too many blue nucleotides.
Your strategy has been added to our implementation queue with task id 32. You can check the schedule of the implementation here.
ETA of the implementation is 6/28/2011
Thanks for sharing your idea!
Dear Eli Fisker
We are glad to report that your strategy has been implemented and tested.
While implementing your strategy, we have made small changes to the parameters you specified to optimize the performance.
Note that we’ll always run a optimization over the parameters you specify, so you won’t have to worry about fine tuning all the numbers you use.
Just the idea and rough numbers are enough to run your algorithm!
Length : Your strategy was implmented with 30 line of code.
Ordering : We ran your strategy on all synthesized designs and ordered them based on predicted scores. The correlation of your strategy’s ordering with the ordering based on the actual scores was 0.10359922179. (1.0 is the best score, -1.0 is the worst score. A completely random prediction would have 0 correlation)
Please note that the numbers specified above will change in future as we’ll rerun your algorithm whenever new synthesis data is available.
More detailed result has been posted on the strategy market page. Thank you for sharing your idea, and we look forward to other brilliant strategies from you!