Highlighting Bases that Switch in the Lab

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  • Updated 7 years ago
I'm not quite sure as to how extensive the changes to the lab interface will be in EteRNA 2.0, however, I would love to be able to see which bases are scored in the switch labs. Whether this is done by highlighting the bases with a "highlight all scored bases" function, or even a list of the bases that are being scored would be nice as well. In addition, if we do go with something like the previous idea, it would be awesome if those bases that got a full point for switching were highlighted as well, that way we can see where in the design bases did not switch, and focus our efforts there. As I said before, I am not sure if any of these ideas are already being implemented for EteRNA 2.0.

As always, thanks for the game :)
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Brourd

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Posted 7 years ago

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Jeehyung Lee, Alum

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Hi Brourd,

All the bases which has experimental SHAPE data (i.e, has a color) contribute to a score. However, unlike the synthesis score in past puzzles which were simply a sum of how right the color is for each base, the switch scoring deploys more complicated methods which takes into accounts how dramatic/right the change in each base is.

Perhaps a right way to approach this is a detailed manual on switch scoring scheme?
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Brourd

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A detailed manual on the switch scoring scheme would be nice. However, I think the main idea I wanted implemented was to have bases that got a full point highlighted, listed, or marked in some way for each design.

As for the highlighting scored bases, that was based on a misconception I had about the scoring for the aptamer loop. Inititally, it seemed like it wasn't scored at all, however, looking at results from previous labs, it seems that the aptamer loop is scored. Am I correct that the locked bases in the aptamer loop are scored based on how the chemical analysis detects the base in the first state?