[Market strategy] GC-content in adjacent multiloops (4 basepairs)

Here is a strategy for our little bot, as I can see he is not sure what to do when around adjacent multiloops. :slight_smile:

I would like a strategy for adjacent multiloops (4 basepairs) that says:

At least 2 of the basepairs should be GC-pairs.

Give -1 if there is only 1 GC-pair

Give -2 if there is 0 GC-pairs.

This is probably not as strict as it should be, but I don’t want to restrain him too much, as I have seen bots succede with less than 4 GC-pairs and Quasispecies made me aware that nature don’t always have 4 GC-pairs in a adjacent multiloop with 8 nt’s long in his post Use RNase P Multiloop Sequences to Create “Cross” Designs. Go see the bacterial sequence.

Picture proof for our bot being a bit confused:

Dear Eli,

Your strategy has been added to our implementation queue with task id 122. You can check the schedule of the implementation here.

Thanks for sharing your idea!

EteRNA team