[Strategy Market] [Switch] Penalize long stems in switching area


As soon as stems in the switching area becomes long, switching becomes harder. I think, as a rough estimate that stems the size of 7 bp and above are generally counterproductive for switching. MicroRNA


Penalize with -1 for each base pair a stem is longer than 6 base pairs. Give a bonus of a 2+ if there is a GU per each 6 bases in stems longer than 6 base pairs.


MicroRNA labs are kind of exceptions, since they need to get some extreme switching going, from not pairing with the microRNA to pairing up with often as much of its 22 bases as possible. So they tend to have really long MS2 gates, like 6-9 base pairs, depending on them being turnoff or turn on labs. They also tend to have 1 GU. So they should be fine despite the penalty. :slight_smile:


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 22 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