[Strategy Market] [Switch] Amount of repeat bases


There seemingly is a difference in amount of repeats, between Turn on labs (same state) versus Turnoff labs (exclusion). So I have made strategies that aims to reward designs with a good percentage of base repeats.

There seems to be a relation between too high or too low amount of repeat bases and few clusters. Not sure what that is about, since we now got A ratio in our designs in a fairly good rate. So I don’t think the repeat A’s are to blame this time. :slight_smile:

The turn on labs seems to need more base repeats than turnoff labs. Those labs have open tail regions which may explain a part of it.


In Turn on labs

  • Reward designs that have a 40 to 50% base repeat.
  • Decrease reward for 35 to 49 and 51 to 55%
  • Penalize for higher or lower repeat ratio.

In Turnoff labs

  • Reward designs that have a 30 to 40 % repeat bases.
  • Decrease reward for 25-29% and 40 to 45%
  • Penalize for higher and lower repeat ratio.

Strategy Background

The natural riboswitches showed a high amount of repeat bases. This is not fully the case for ours yet. Part of it may be due to limits of amount of repeat C’s and G’s, there are longer stretches of these in the natural riboswitches.

However while I expect the repeat bases to grow in prominence and importance, I have made a strategy for now.

What I basically wish it to judge is what amount of single bases there are compared to repeats of the same color. Like what is normal amount of single A’s to A repeat bases in top scorers.

I see turnoff labs behave differently from turn on labs so I have made separate strategies. Similar I see microRNA labs behave different from the other MS2 labs, so I have separated those too.

The amount of repeat in the microRNA designs are going to be dependent too of how much repeat there are in the microRNA sequence itself. But even there I think there will be a somehow good ratio.

Background articles

Different types of switches

Entropy, repeat bases and natural riboswitches

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 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