[Strategy Market] [Switch] How MicroRNA likes to bind: Turnoff labs

Strategy Market Strategy Market - Switches
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Intro

It is not just switches that are different from static designs, also microRNA labs wants different things depending if they belong to the turn on or turnoff variant. :slight_smile: Therefore a specific strategy for turnoff microRNA labs.

Strategy - Give + 3 if 18-19 of the microRNA bases are complementary bound to the RNA design. Subtract a point for each more or less base binding. - Give -1 for each of the base pairings that do not use the strongest possible match (eg a GU when a GC is possible or a GU when an AU is possible. Except at two first and two last of the basepairs from each end of the microRNA. The ends are allowed to pair weaker. So give only 1ā„2 penalty there. - Give -1 per each, if microRNA bases 12-14 is paired. MicroRNA bases that should preferably pair up with the design: 1-11 and 15-22 The winners seems to have microRNA base pair for around 18 base pairs.

Background articles https://getsatisfaction.com/eternagamā€¦https://getsatisfaction.com/eternagamā€¦https://getsatisfaction.com/eternagamā€¦https://docs.google.com/document/d/1Aā€¦

1 Like
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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

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Dear Eli Fisker,

I am pleased to announce that a preliminary version of your strategy has been implemented with 53 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