[Strategy Market] Berex Loop Basic

Can implement it as its own strat, would also like to see the difference it makes to my test strat.


Hi Berex, can you clarify some stuff for implementation?

  1. internal bulge - has a GC partner

I’m not sure what you mean by this…can you throw in an example?

  1. Can you clarify what you mean by “top” and “bottom” in N-N loop specifications?


  1. Internal Bulge
    Shown by the following two examples

  1. In any loop, the side with the fewer nts, is considered the bottom of the loop.

Berex, thanks for the clarification!

Your strategy has been added to our implementation queue with task id 7. You can check the schedule of the implementation here.

ETA of the implementation is tomorrow 6/4/2011

Thanks for sharing your idea!

EteRNA team

Berex, could I ask for little bit more clarification for loops with 5+ bases?

For example, if you have a multi-loop of 10 bases, would you give +2 points as long as it has 2 Gs in it regardless of exactly where those 2Gs are?

(Same question when we have internal bulge of 5+ bases, hairpin loop of 5+ bases…etc)

We are sorry that this is taking a long time, but we want to get the algorithm as good as possible!

Sorry I must of missed this reply.
Multiloop of 10 bases, both G’s must be on the same side.
For simplicity sake, I was only going to count it regardless of where it was.

Hairpins follow the tetra rule, only one G
For Internal Bulge’s, should only be max 2 G’s in it.

Dear Berex,

We are glad to report that your strategy has been implemented and tested and also very sorry about the late implementation!

Length : Your strategy was implmented with 70 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 0.073. (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!