I like to ad a strategy that says, no strands with 3, 4 or more blue nucleotides in line. Penalize for each extra with -1.

Dear Eli,

Your strategy has been added to our implementation queue with task id 29. You can check the schedule of the implementation here.

ETA of the implementation is 6/24/2011

Thanks for sharing your idea!

EteRNA team

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 **45** 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 **0.125296272355**. (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!

I will like to add that while I don’t like lines of blue of 3 and more on stems, they will sometimes be legal. In particular in bigger designs with real long stems. I still don’t think they are a good idea, but they will sometimes be allowed. So I will add, give half penalty if the blue line is in a 9+ base pair stem. But since it also matters where it is placed, and I don’t want this give a backdoor to trouble, give double penalty if the blue line touches closing base pair or next base pair.

thank!!