[Strategy Market] [Switch] JL’s microRNA fish hook 2: MicroRNA landing spots

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Intro

This strategy is courtesy to jandersonlee and based on his superior round 1 microRNA design strategy, that ended hitting through among the majority of the winners in the following round too.

Strategy for Turn on labs microRNA positioning

  • Give +2 for each base of the full microRNA that pairs up in the space between 6 and 28 bases after the MS2.

  • Penalize designs that makes the main part of the microRNA bases, pair up before the MS2 sequence into oblivion. :slight_smile:

Purple1jpg
Image: https://lh3.googleusercontent.com/HttMvm3cxlrMFXZxVM1moTONHv-e3-1bGy3HzsAImXPOEQHa6_kE2zXmbe_b6vxf1jT9h1FOxsRVN6fnT9GEQVWNOKYrInv8riAnBRXXMuH22ALIQiLUbQVwDEOdoGmmJ-n4zA1600×1163 215 KB

Strategy for microRNA turnoff labs

I wish to reward designs that has each end of the microRNA pair up on each side of the MS2 sequence.

MS2 in early half of the RNA sequence

  • Give +2 for each base of mir 2 sequence (of the last 8 last bases of the microRNA) that pairs up 8-14 bases before the MS2 sequence. (These 6 bases between MS2 and mir pair up leaves room for the MS2 to get a proper turnoff sequence)

  • Give +2 for each base of the mir 1 (earliest 11 bases of the mir) that pair up after the MS2 sequence. Region for pair up: The last base of the MS2 sequence and the 11 bases after.

Image: https://lh6.googleusercontent.com/1KiirWzsxteXALEzONfv5eqkywDlh5Eq8uhNhmAJTcxkwoqIl9tzhNx7kwkI3xqbmx60-tDiqZcJYpSHvjzWaUqu8uwa2Syc04FZbmZAyk3VbbO1tDqF8ggrBcO93evR5Jur8A1600×1163 209 KB

MS2 in late half of the RNA sequence

  • Give +2 for each base of mir 2 sequence (of the last 8 last bases of the microRNA) that pairs up 2-14 bases before the MS2 sequence

  • Give +2 for each base of the mir 1 (earliest 11 bases of the mir) that pair up after the MS2. In the region of 6-8 bases after the MS2. (These 6 bases leaves room for the MS2 to get a proper turnoff sequence) Region for pair up between mir and design 6-19 bases after the MS2

Image: https://lh3.googleusercontent.com/s8EDdmKtk-hDQmDRaceJ9XpGzQ-I03p8lfTkOzXMbyzA8C_PO7F4dYiq6fc01w8OhpwhM2_Ykq7kit9D5CMm9K-ecR5OcIaWjB2VRRUSdBPUOxfeDLojnp2oPYtq-h3LCoBS-g1600×1163 213 KB

Background articles

Imagining the microRNA labs

[https://getsatisfaction.com/eternagame/topics/johan-s-microrna-lab?topic-reply-list[settings]filter…

[https://getsatisfaction.com/eternagame/topics/johan-s-microrna-lab?topic-reply-list[settings]filter…

[https://getsatisfaction.com/eternagame/topics/johan-s-microrna-lab?topic-reply-list[settings]filter…

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 52 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