[Strategy market] Placing of boostpoints in bulges

Definition: Boostpoints - Placing of red, green or blue nucleotides in multiloop ring, hook area or bulge, in a spot where it changes the energy level inside.

I think that boost nucleotides in bulges only do good, if next to one of the closing basepairs. These are the places, where a boostpoint usually have the power to change energy inside the bulge. The legal places for placement are represented by the red nucleotides in the pictures - if it changes energy.

Illegal spots
If blue, red or green nucleotides are placed in the bulges outside of the legal spots (reprecented by the A’s.) give -0,3 pr each extra.

Legal spots
Also, allow max. 2 boostpoints used pr. bulge. Give -0,3 pr extra.

Dear Eli,

Your strategy has been added to our implementation queue with task id 51. You can check the schedule of the implementation here.

ETA of the implementation is 8/31/2011

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 52 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 0.0160435101359. (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!

Brourd discovered today when he ran my strategy, that the predicted score for all designs were 100. Which means the strategy is not generating a predicted score. Just wanted to say. Best wishes.

Brourd also made me realize that I made some faults in the strategy.

I would like to start the base score line at 95, instead of subtracting from 100.

Also I will like to penalize harder. Instead of -0.3 pr. illegal placed boost, give -1 pr. each.

Hi Eli.

I noticed that not every predicted score is 100. As you go to the bottom, you can see some of the predicted scores are not 100.

Currently, the algorithm is subtracting 0.3 when red, green and blue is not placed on boostpoint of bulges. Also, it subtracts 0.3 whenever the number of boostpoint in bulges exceeds 2 (as long as the boostpoints are colored in red, green and blue).

Let me know if there is any error in the algorithm.

I will also set the base score line at 95.


Hi Sebon!

My mistake. Can you set the penalty to -1 instead of -0,3 too?

Big thanks for the correction.