[Market strategy] Boost or no boost depending on loopsize

Hairpins with tetraloops and pentaloops mostly seem to be fine without boosting. (Strings 4 nts and longer) However hairpins with loops bigger than a pentaloop, some sort of boost seems to be necessary. (Strings 4 nts and longer) It appears a GC-pair at the end of a string is not enough to hold a loop of 6 nucleotides in spot, if they are all A’s. Often 1 or 2 of the nucleotides i the loop ring end up with a blue color dark enough to suggest they paired up somewhere - unwanted. I still don’t know what sort of boosting is correct here, just that some seem to be needed.

As I’m not sure which kind of boosting that is required, so I want a strategy that opens up for it in this special boosting, but not too much. I just want this situation penalized less, as I can see a potential need for boost here.

As we already have all A’s loop strategy and the boosting in bigger loops is what I’m after, I would like a strategy that says:

Give +1⁄2 if there is up to 2 different colors boosting, in loops 6 nts and longer (on strings 4 nt’s and longer.) I don’t know about position yet, so this strategy will need an addition.

This is related to the post I wrote earlier about Boost according to lenght of hairpin.

Dear Eli,

Your strategy has been added to our implementation queue with task id 123. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team