[Market strategy] Double sameturning pairs with multiloop junction.

Strategy Market Strategy Market - Single State
1

Earlier I made a strategy to minimize the use of double sameturning pairs, with max one pr symmetric design and two for asymmetric as they mostly causes trouble. I didn’t specify where they were allowed. It seems that they cause worse trouble, if they are not inside a string, but is placed in connection with a junction.

I would like a strategy that says :

Ban with double sameturning AU-pairs, if placed in connection with a junction. That also counts if they are placed in a juction in connection with an adjacent multiloop. Neckarea is excepted from this strategy. For some reason double sameturning GC-pairs is not always as bad, though

Give – 1 pr each of double sameturning AU-pair, if in connection with a multiloop junction.
Give -0,25 pr each double sameturning GC-pair, if in connection with a multiloop junction.
Give – 3 for double sameturning GU-pairs, if in connection with a multiloop junction.

Also there seem to be difference between multiloops and hairpin loops. Hairpin loops is less penalized if a double sameturning GC-pair is placed there, compared to if in the multiloop.

Give half penalty for double sameturning pairs if the junction is not a multiloop junction but another junction.

2

Dear Eli,

Your strategy has been added to our implementation queue with task id 121. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team

3

Just to make sure there is no misunderstanding as my pictures are not accurate. Those are just showing the double sameturning pairs, but not in connection with a junction.