[Strategy Market] GU placement

Strategy Market Strategy Market - Single State
1

This strategy should penalize GU-pairs harder in short strings than in longer, where they are better tolerated. It also match what I have seen work in lab. Not in all cases, but in many.

I would like a strategy for GU-placement that says:

Give + 2: No GU-pair next to closing basepair, except if the closing basepair is a GC-pair. And the energy in the quad is -2.5. Give + 1 if this is the case.

Give + 2 No GU-pair as closing basepair, unless the basepair next to the closing GU is a GC-pair. And the energy in the quad is -2.5. Give + 1 if this is the case.

Only dispensation is if the next pair is an AU-pair and the energy of the quad is -1.4. Then give + 1.

2

Dear Eli,

Your strategy has been added to our implementation queue with task id 143. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team