[Strategy market] Green and blue nucleotides a strand + Strong middle half

Strategy Market Strategy Market - Single State
1

This is an addition to my strategy Green and blue nucleotides on a strand, where I take in to account, that a strengthening appears to be taking place right after the middle of the design. (For the theory behind this see my getsat post Slightly skewed energy tendency for the whole lab)

So this strategy should be excactly as my Green and blue nucleotides on a strand, with the only exception, that I allow a blue/green line on a strand that is one nucleotide longer than stated in my strategy - if this longer blue/green line is found up to 11 nucleotides after the exact middle of the design (this 11 nt limit may have to be higher, if we are starting to making bigger lab puzzles)

So here my strategy is again with the addition.

I would like to ad a strategy about how many blue and green nucleotides I will allow in line right after each other on a strand of a certain length.

In a string 3 nt long, allow max 3 blue/green nt in line on a strand
In a string 4 nt long, allow max 3 blue/green nt in line on a strand
In a string 5 nt long, max 3
In a string 6 nt long, max 4
In a string 7 nt long, max 4
In a string 8 nt long, max 4
In a string 9 nt long, max 4

In neckarea up to 6 is allowed. (including this number)

Penalize with -1 for each extra blue/green nucleotide above the number allowed,

Except if one extra nucleotide is found in the area (number of nucleotides divided with 2 and found between this area and + 11 nucleotides)

2

Dear Eli,

Your strategy has been added to our implementation queue with task id 36. You can check the schedule of the implementation here.

ETA of the implementation is 7/3/2011

Thanks for sharing your idea!

EteRNA team

3

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 190 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 0.00544063779358. (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!