[Strategy marked] Adjacent multiloops with non-adjacent stacks

I think I see a tendency for multiloops with a mixture of adjacent and non-adjacent stems. While the closing basepairs for the adjacent stem can follow usual orientation or have red facing each other and green too, the closing basepair for the non-adjacent stem seem to be following usual orientation.

Also if they occur as closing basepair in a neck. A place where the closing basepair have a tendency to be allowed to be flipped both ways. The lab An arm and a leg, is an example of a lab where the neck is also the non adjacent stem in a multiloop with adjacent stems.

Since I think non adjacent stems in this type multiloop behave a certain way compared to the non adjacent, I thought I wanted to make a strategy.

Give + 1 if closing basepair follows the orientation shown above, for the non adjacent stem in the multiloop.

In general the energy model suggests that a GC like this is among the strongest ways to close a non-adjacent multi-loop stack, unless it is backed by GU, in which case it is not quite as strong. I’d say +0.5 for GC backed by GU and +1.0 for all other combinations (UG, AU, UA, GC, CG).

And while we are at it, +0.5 for CG backed by (CG, UG, UA, or AU) and -1.0 for any closure by UG.

Perhaps this change should be an alternative strategy rather than an update to this one since it is based on the energy model rather than your examination of lab data?

Hi JL! I will like to see the full strategy run with your addition too. When we have more lab data on this, we can always add changes, should there be some things that needs to be adjusted.