I would like a strategy that says, no blue nucleotide allowed if not paired up with a yellow nucleotide in a AU-basepair.
This strategy is in family with earlier strategies of mine, banning blue nucleotides in multiloop ring and hook area. But this might be a smarter way to reduce the numbers of strategies and eliminate use of blue nucleotides in bulges and smaller loops too.
For each blue nucleotide not paired up (alone – placed in outer loops, internal loops, multiloop, bulges and hookarea, give -1 pr. each.
Ignore blue nucleotides paired up with red in GU-pairs, as there are other market strategies trying to take care of this. Or give -2 pr. each.
Hi Eli - so no Us in the loops - is this correct?
Your strategy has been added to our implementation queue with task id 61. You can check the schedule of the implementation here.
Thanks for sharing your idea!
Yes, that’s correct.
I’m aware that in eg. tetraloops, a couple of blue nucleotides might be allowed. But it will be easier to add exceptions for these cases later, when we find out which ones might be ok.
Dear Eli Fisker
We are glad to report that your strategy has been implemented and tested.
While implementing your strategy, we have made small changes to the parameters you specified to optimize the performance.
Note that we’ll always run a optimization over the parameters you specify, so you won’t have to worry about fine tuning all the numbers you use.
Just the idea and rough numbers are enough to run your algorithm!
Length : Your strategy was implmented with 0 line of code.
Ordering : We ran your strategy on all synthesized designs and ordered them based on predicted scores. The correlation of your strategy’s ordering with the ordering based on the actual scores was 0.231385267059. (1.0 is the best score, -1.0 is the worst score. A completely random prediction would have 0 correlation)
Please note that the numbers specified above will change in future as we’ll rerun your algorithm whenever new synthesis data is available.
More detailed result has been posted on the strategy market page. Thank you for sharing your idea, and we look forward to other brilliant strategies from you!