Strategy
Penalize end loops that has low energy in loops in hairpins that participate in the switching area.
For hairpin loops in the switching area, at 5 base pair and longer, reward if the end loop has high positive energy and penalize increasingly the more negative the energy becomes.
For hairpin loops in the switching area, at 4 base pairs and shorter, reward up boosting.
Background
I’m not entirely sure that basing this strategy on an observation of a pair of designs with few clusters is valid.
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 26 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