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vineetsk1 / Switch-Strategies

Implementations of the strategies for Eternabot switches.
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[Strategy Market][Switch]Predicted probability of MS2 hairpin fully forming #10

Open vineetsk1 opened 9 years ago

vineetsk1 commented 9 years ago

Original Author: Omei Turnbull Original Link: https://getsatisfaction.com/eternagame/topics/-strategy-market-switch-predicted-probability-of-ms2-hairpin-fully-forming

From the dot plots produced by ViennaFold 2.2 for the ON and OFF state, pull the probability of the pair forming at the base of MS2 hairpin. Here's a picture to illustrate the pair, but the exact base numbers will depend on where the hairpin is in the submission.

If the probability in the ON state is below a threshold TBD, deduct a penalty. If the probability in the OFF state is above a (different) threshold, deduct a different penalty. Presumably, these thresholds and penalties will need to be calculated independently for the switch direction and type of aptamer (MS2 vs miRNA).

My expectation is that this will be useful for weeding out some poorly scoring designs, but not particularly useful for distinguishing great designs from mediocre ones. Thus, the most effective thresholds will probably be fairly tolerant ones.

For an explanation of why I'm nominating this, see Dot Plot / melt plot converted to data.

vineetsk1 commented 9 years ago

Implemented with 17 lines of code.