Slide the sequence past itself in reverse one base at a time and determine how many pairs form each time.
e.g. for the sequence
we would get 6 pairs for the first iteration:
\*\* \* \* \*\*
8 pairs for the second:
\* \*\*\*\*\*\* \*
6 for the third:
\* \*\* \*\* \*
and so on.
Penalize the design for each pair. Optionally give different penalties for different types of pairs (AU, GU or GC). It would probably also be wise to subtract the number of intended pairs from the total.
Your strategy has been added to our implementation queue with task id 25. You can check the schedule of the implementation here.
ETA of the implementation is 6/22/2011
Thanks for sharing your idea!
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. Specifically, we limited the maximum shift to 3 bases.
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 30 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 0.399. (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!
Just curious, did you adjust the penalties according to the total length of the sequence (i.e. a sequence that’s twice as long gets penalized half as much per pair)? If not, does doing so improve the results?
yes - penalties have been normalized by dividing them by the sequence length,
We have also updated your strategy with the latest “The Asymmetry” results. check it out!