[Strategy market] Double sameturning GC-pairs

Strategy Market Strategy Market - Single State
1

I would like to ad a strategy about what to do, if a double sameturning GC-pair are found together like this:

  • One of these double GC-pairs are allowed with out penalty (1 pr. string), if found in a string more than 6 nucleotides long.

  • Up til two of these are allowed without penalty in the neckarea, if not next to each other, else penalize with -1

  • Two sameturning GC-pairs are to be penalize with -2 if found elsewhere in the design.

Some of the rules are sloppier in asymmetric designs – in designs with asymmetric (whole) arms like The asymmetry, Bends and ends and A tilted picture of running man. This also happens in designs with different numbers of nucleotides between multiloop arms. (The asymmetry)

  • So in those type of asymmetric puzzles, allow one sameturning double GC-pair in the design without penalty and two in the neckarea.
2

Dear Eli,

Your strategy has been added to our implementation queue with task id 39. You can check the schedule of the implementation here.

ETA of the implementation is 7/19/2011

Thanks for sharing your idea!

EteRNA team

3

Cheng asked a question about my strategy, that made me realise I was wrong about a part of my strategy. I wrote:

Up til two of these (double GC-pairs) are allowed without penalty in the neckarea, if not next to each other…

Then I remembered Hurshy’s branches design A real attempt

Here two double sameturning GC-pairs were right beside each other (to the left, basepair 9-12/93-96) and the neck were perfect as there were no mispairings:

It is rare though. But allowed in the same pattern as more than one doubleturning AU-pair in a neck. Again an example that the neck is it’s own special area. This pattern (and overall high energy) would not be allowed in the strings in the design.

So if two double GC-pairs are found next to each other, they need to be twisted compared to each other, just like here, else penalise with -1

And up til 3 double sameturning GC-pairs are allowed in the neck without penalty.

4

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 247 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 0.0196884214437. (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