[Strategy Market] [Switch] Element: Distance between MS2 and aptamer sequences

Strategy for turn on labs (Same State)

For when MS2 sequence is in between the FMN sequences

Give bonus if there are 11 single bases or less at the shortest side between the aptamer on either side and the MS2 sequence. Add more bonus if the shortest side is like 5-6 bases long. Penalize for single bases stretches longer than 11 bases on either side and if shorter than 6 bases away.

For MS2 on the outside of the FMN sequences

Reverse the strategy. So best bonus is given to distance 11 bases apart and decreasing towards 6 bases. (Same state 1) Penalize for single base stretches that are shorter or longer than 6-11 bases.

Strategy for turnoff labs (Exclusion)

Give +3 for MS2 being next to FMN and decrease the bonus by one for each base the MS2 moves away from the one FMN it is closest to.


A popular strategy to achieve a shortening of the space between MS2 and FMN is to abbreviate the stretch of single bases by making them form a stem with themselves. But before I make a strategy for it, I wish to know if the trick can be done by simply cutting the bases out (We should get those data with the NG labs where we could vary distance between MS2 and FMN) or if the Static stem play an active and positive role in itself.



1 Like

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

Dear Eli Fisker,

I am pleased to announce that a preliminary version of your strategy has been implemented with 30 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