[Strategy Market][Switch] Penalize large amounts of GC pairs

Note: This is an example of strategy submission in the EteRNA Strategy Market

My strategy is to look at the percentage of GC pairs in the design. I think that a large number of GC pairs would prevent the secondary structure from switching states. Based on this, I would penalize designs that have more than 40% GC pairs and award designs that have less than 40% GC pairs but more than 20% GC pairs.

Please implement my strategy!


This is specific to the FMN switches.

By “half-aptamer structure”, I mean that the FMN aptamer internal loop, in the NOFMN state, is closed by a stem of at least three pairs, and the bases on either side of the helix are unbound. If that’s ambiguous, perhaps A Structure Design Pattern for Eterna MS2 Riboswitches will help.

If the Near Half-Aptamer structure, but not the Far Half-Aptamer structure, is present in the predicted MFE structure for the NOFMN state, add a bonus.

If the Far Half-Aptamer structure, but not the Near Half-Aptamer structure, is present in the predicted MFE structure for the NOFMN state, add a different (probably smaller) bonus.

If both are present in the NOFMN state, apply a penalty.

How to make a strategy for the Strategy Market

I realized that many of you guys have not tried making strategies for the EternaBot before. So here is a little help.

It is far from as complicated as it may sound. You can help without being a programmer. (Being a programmer won’t hurt you either.)

What to look for to make a strategy

If there is just one thing that you see good switches have, but bad switches doesn’t, then it could be worth a mention. That’s basically what strategy making is. Its as simple as that. Pointing out areas of interest. The Bot doesn’t know what is important, before getting told so. However when knowing where to look for something, it can do machine learning on it.

What to do

Give it points, say what to penalize or reward.

The numbers don’t have to be totally exact, just give a good estimate. Here is how the developers (In this case Jeehyung Lee) encouraged us last time:

_While implementing your strategy, we have made small changes to the parameters you specified to optimize the performance.

Note that we’ll always run an 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!_

Market Strategy Example

Thx Vineet, for your fine strategy example!

Here is one more example of how a strategy can be made. It is fairly simple.

[Strategy market] Numbers of yellow nucleotides pr. length of string

It was one of the strategies that ended up in EternaBot.

Short is good, so don’t do as I sometimes tend to do… :slight_smile:

Lets help our EternaBot become a good SwitchBot! :slight_smile:


Want more examples? You can find them in the forum by searching for [Market Strategy]. Since all the latest strategies are obviously going to be switch ones, you can find the static design ones by picking among early submissions.

For more inspiration on lab analysis, see My Lab Analysis Kit. (I can’t link directly, but searching with the phrase will take you to the section.

Dear vineetkosaraju,
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 vineetkosaraju,

I am pleased to announce that a preliminary version of your strategy has been implemented with 4 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