[Strategy Market] Adjacent U's and C's

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  • Idea
  • Updated 8 years ago
In stacks of any length, award points to an RNA anytime an AU pair is adjacent to a GC pair on the end or beginning of the stack if the Uracil is adjacent to the Cytosine. That is, for example, that the U of an AU bond would be NT# 7, and the C of a GC bond would be NT#8.

For an example, here's a picture:


Note that first string from left to right. Whenever the Uracil is adjacent to the Cytosine of a GC/AU stack with the GC being on the end of the string, the RNA tends to become more stable, and gains negative free energy. However, this trick does not seem to apply whenever the GC pairing is not the endpair, and, in fact, seems to weaken the fold when in the middle of the string. That considered, you may choose to not reward (and, in fact, penalize) C-U adjacencies in that situation, though this may obviously be reversed, depending on what is desired.
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paramodic

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Posted 8 years ago

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Jeehyung Lee, Alum

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Dear Eli,

Your strategy has been added to our implementation queue with task id 113. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team
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paramodic

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Jee!