[Strategy Market] Repetition

Measure how many times each subsequence of length n is repeated in the whole sequence for each n in some reasonable range, e.g. from 2 to 5. For our purposes let “the number of repetitions” be defined as “one less than the number of occurances”, i.e. if GA occurs 3 times we say it is repeated twice.

For example, for the sequence


we get 1 repetition each of UC, CG, GUC and CGU and 2 repetitions of GU.

The design is penalized for each repeating subsequence based on the length of the subsequence and the number of repetitions.

Dear aldo,

Your strategy has been added to our implementation queue with task id 24. You can check the schedule of the implementation here.

ETA of the implementation is 6/21/2011

Thanks for sharing your idea!

EteRNA team

Dear aldo

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 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 -0.107976653696. (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!