Take your string of aaccuuguuaa etc, stick it into vienna, get the centroid** shape notation
…((…))… etc, paste that into the puzzle builder, paste your sequence of bases back in,
** = Take the centroid at the lowest temperature that the centroid shape is not the same as the target shape.
This strategy assumes that the more red the centroid shape is - the harder and less likely it is to go to the centroid shape, so that should mean it’s more likely to stay in the target shape.
so more red in the centroid = give it more points
might need a flat meltplot too before this becomes interesting - but I’ll try that as a seperate strategy for now.
That may not be implementable in eteRNA because of the fact that it does not calculate the centroid secondary structure like the ViennaRNA server does.
yes sure, doesn’t have to be vienna as such, but any centroid shape generating program that the Eternals (coders) can whip up or access would do.
Your strategy has been added to our implementation queue with task id 100. You can check the schedule of the implementation here.
Thanks for sharing your idea!
Maybe penalize structures according to the base-pair distance between the MFE structure and ensemble centroid?
It sounds like it might make sense - but perhaps that should be a second seperate strategy to not cloud any inference by having too many factors ?
I’m not opposed to adding it to this one - it’s already at the edge of my understanding so I’ll go with the opinions of the wiser Eternals such as yourself - as to whether this should be in the same or a second strategy
Oh, that’s fine. Sorry if you though I’m trying to detract from your strategy. I was more hoping bounce ideas off of people.
Anyway, I think I misunderstood what you were trying to do, since you’re changing temperature to force the ensemble centroid to differ from the MFE structure.
As far as “wisdom” goes… it’s probably overrated in this game. I think that the insights of people who aren’t constrained by “conventional wisdom” are a huge strength of the EteRNA community. And I really doubt I possess much in the way of “conventional wisdom” to begin with. RNA isn’t my field, and I’m still very much a biochemical padawan in a world full of Jedi.
Well the trouble with not forcing the centroid to differ for my scheme is that any build I have that works for the MFE would automatically work perfectly for the centroid. But you have pointed out that the temperature required to make the centroid not equal the MFE should be added as a second strategy market.