# [Market strategy] Even energy distribution in design (neckarea excluded)

I would like to ad a strategy that says, that energy difference between strings of same length must be highest 5%.

Eg. Branches designs have:

4 arms which is four nucleotides long
2 arms that are five nucleotides long

The energy difference between arms of same lenght must be max 5% difference between the arm with lowest collective energy and the arm with highest collective energy.

Penalize with -1 for each 1% higher than 5 % energy difference between arms of equal size.

And ad up for different lenghts of arms:
4 arms, 4 nucleotides long - 8% difference (3% over 5%)
2 arms, 5 nucleotides long - 7% difference (2% over 5%)

3% + 2% = 5% Penalize with -5

Dear Eli,

Your strategy has been added to our implementation queue with task id 37. You can check the schedule of the implementation here.

ETA of the implementation is 7/12/2011

EteRNA team

Hi Eli,

Can you explain how “arms” are defined? In general, we need all terms with specific definitions to have algorithms implemented.

Thanks!

Hi Jee

Ah, I see where the problem is. With arms I did not mean the whole arm in eg. a four armed design. Here I meant string/stem. Where RNA is double stranded.

I will like to have the tolerance for energy even energy difference set higher. To a max 20-25 % difference between the string with the lowest energy concentration (compared to length of string) to the string with the highest energy concentration. I think I got it set too low before and having it too low will exclude many good designs. Even energy distribution seem to be the rule for good designs, but it is a more extreme energy difference between parts of a RNA design that will make a design do bad.

I think there is a local part of this strategy, that should ensure that local elements like strings don’t have uneven distributed energy, like a 4 nt long string having either all GC-pairs or all AU-pairs.

Then there is a global part of it. But here is a bit more about how the global part of it could be made, if I look at the energies in the quad. Quads have energies between -0.9 to -3.4. That is a difference on 2.5. If I divide that with 4, and add a fourth of that to both the low energy quad and the high energy quad, I have an energy area between -1.53 to -2.8 which is relatively safe for a design to be in. And a bottom and top energy area that I don’t want the designs to be in.

If a good mean for global energy distribution could be established, perhaps it could be used to catch energy violations. Imagine that the mean energy for an element like a string is -3.4 (christmas tree) or -0.9 (cub scout). Then the difference in good global energy for a design (can be a number or an interval of numbers, to ease calculation for our bot) can reveal that the local mean is way off.

And as I see I didn’t put in a link to the theory behind this strategy, when I made it, here it comes. Theory of even energy distribution - Energy, structure and symmetric colors