[Market strategy] GU-pair in a junction

If a GU is placed in a junction, the energy between it and the next basepair in the string shall be in a certain range. (if that is hook end of the neck or multiloop end of a neck or near any type of loop. 1-1 included – but bulges excluded)

I would like a strategy that in case a GU-pair show up in a junction says:

Give 0 if energy is -2.1 and -2.5 or between that GU-pair and the next basepair

Give 0 if energy is -1.4

Give -1 for other energy values than the above mentioned.

Dear Eli,

Your strategy has been added to our implementation queue with task id 117. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team