I would like to ad a strategy for numbers of yellow nucleotides allowed pr. lengt of string (neckarea excluded):

If a string/arm is this number of nucleotides long, then allow this number of yellow adenine. For each yellow nucleotide below the minimum or above the maximum, penalize with -2.

String length (yellow nucleotides)

3 (1-2) String eg. the bulged cross and the asymmetry

4 (1-2)

5 (1-3)

6 (2-3)

7 (3-4)

8 (2-5)

9 (1-4)

This could be used to rule out some of the cub scouts and a few christmas threes.

Dear Eli,

Your strategy has been added to our implementation queue with task id 25. You can check the schedule of the implementation here.

ETA of the implementation is 6/23/2011

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 **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 **0.199598735409**. (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!

Similar strategies could be made exactly the same way as I mention here, for the blue, red and yellow bases.