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

Strategy Market Strategy Market - Single State
1

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

2

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

3

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:

Don’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/eternagam…