[Strategy Market] [Switch] Base relationship between non repeat bases

Strategy Market Strategy Market - Switches
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Intro

As I were looking repeat bases in top scoring switch designs, I noticed that there seemed to be a relation between amount of single bases in relation to each other. There generally were more single A’s than single U’s, more U’s than single G’s and C’s. And there tended to be more G’s than C’s, although not always. (When I mention single here, I do not look at weather they are paired or not, I’m only looking at that they are not repeat bases.)

There were more single A’s and U’s than single C’s and G’s together. No surprise about the relation there, since this reveals relation of Watson Crick base pairing. :slight_smile: Also it seems that there can’t be too big different in amounts of the different bases.

Strategy

  • Reward when there are more single A’s and U’s when summed, than single C’s and G’s summed

  • Reward when there are more A’s than U’s, more U’s than G’s and more G’s than C’s.

  • Reward when the relationship between bases are as following: There can’t be more than 8% difference between any of the single bases in amount.

Along the lines of my earlier repeat base strategy, there can’t be more single bases than 60-70 % for turnoff labs and 50-60% for turn on labs.

2 Likes
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Dear Eli Fisker, 

Your strategy has been added to our implementation queue and we should have it completed within the next two to three weeks. You can check the status of the implementation here.

We will also be uploading the code used to write your strategy on this page if you are interested in reading it later.

After implementing your idea, we will post the direct link to the code here. Then, we will then optimize the parameters, and test it. At that point, we will tell you the correlation of how good your strategy was and what the new optimized parameters are.

Thanks for sharing your idea!

Vineet Kosaraju
The EteRNA Team

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Dear Eli Fisker,

I am pleased to announce that a preliminary version of your strategy has been implemented with 23 lines of code. The code might slightly change in the future to remove bugs, but you can check the current version here. We will soon work on optimizing your parameters and testing the strategy.

Thank you again for sharing your switch strategy!

Vineet Kosaraju
The EteRNA Team