# [Market strategy] Direction of GC-pairs in small and big multiloops (symmetric)

I would like to ad a strategy about size of multiloop

Symmetic multiloop = multiloop with same numbers of nucleotides between the multiloop arms.

Here is my hypothesis: Tolerance for opposite direction of GC-pairs in a multiloop, sometimes have to do with size of multiloop. In smaller multiloops there is a greater tolerance for opposite turning GC-pairs than in big ones.

In multiloops with 4 nucleotides between the arms, if a GC-pair in the multiloop turn opposite in another possition than the neck, give -5 pr each extra

In multiloops with 3 nucleotides between the arms, if a GC-pair in the multiloop turn opposite in another possition than the neck, give -4 pr each extra

In multiloops with 2 nucleotides between the arms, if a GC-pair in the multiloop turn opposite in another possition than the neck, give -3 pr each extra

In multiloops with 1 nucleotides between the arms, if a GC-pair in the multiloop turn opposite in another possition than the neck, give -1 pr each extra

In multiloops with 0 nucleotides between the arms, if a GC-pair in the multiloop turn opposite in another possition than the neck, give 0 pr each

For theory behind this see the post Our kid robot

Dear Eli,

Your strategy has been added to our implementation queue with task id 54. You can check the schedule of the implementation here.

ETA of the implementation is 9/5/2011

Thanks for sharing your idea!

EteRNA team

There is an update to this strategy. We now have much more data on even bigger multiloops (symmetric or non-adjacent ones) and they do behave differently.

So if I would make the strategy different today.

For small multiloops with an average 1-4 single bases between stems:

Give + 1 if GC-pairs turn in usual orientation. Give -1 for each opposite turning GC-pair. (Having a few reverse is regularly legal. So is having non-GC-closings also, in particularly at neck closing.)

For bigger multiloops with an average of 5+ bases between the stems:

Donâ€™t give any minus points for opposite turning basepairs. Give + 2 if there is some.

(The four way multiloop (0-0-0-0) needs its own strategy as it behaves a lot different. Similar adjacent multiloops behave differently to the symmetric ones.)

For more behind this idea, read here:
https://getsatisfaction.com/eternagamâ€¦