I would like to ad a strategy, that penalizes basepair similarity. Give -1 for each basepair that is same colors and turn the same way as it’s neighbour.
In this strategy I will just aim at penalizing sameturning basepairs, though I’m aware that they are allowed under certain conditions. I have made other strategies (not programmed yet) that opens up for use of double AU and GC pairs at certain places.
This is just the broad strategy to bomb out designs with too much repetitative, sameturning basepairs, no matter what their color are and length of numbers of them in line. This is because very few of the really good designs have them.
Usually two repetative basepairs are allowed in the neck, only one in the main design and sometimes two in the main design - if it’s an asymmetric design. I’m aware that the really longarmed designs like the cross, have a greater tolerance for repetative basepairs. In strings 8 and more nucleotides long, 2 similar sameturning basepairs are allowed pr. string, exactly like in the neck area. I just wanted to keep this strategy simple.
Your strategy has been added to our implementation queue with task id 40. You can check the schedule of the implementation here.
ETA of the implementation is 7/15/2011
Thanks for sharing your idea!
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 15 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 0.176777878387. (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