I would like to ad a strategy that says, there can be 0 or 1 double AU-pair in the design (two AU-pairs turning the same way.) For more than one double AU-pair, ad -1 pr. extra.
Neckarea is the exception to this strategy. Here up to 2 X 2 double AU-pair are allowed (if these quads are switched opposite to each other.) Au-pairs in the neck are not counting as AU pairs in the overall design. If there is two double AU-pair in the neck, then an additional AU pair is allowed elsewhere in the design, without penalty.
Dear Eli,
Your strategy has been added to our implementation queue with task id 18. You can check the schedule of the implementation here.
ETA of the implementation is 6/18/2011
Thanks for sharing your idea!
EteRNA team
I read the numbers in the new bot results, as each strategy with a minus in front of the number, tells me that patterns from the other strategies in the ensemble algorithm, violates this strategy. (Not all strategies can be happy at the same time) Each positive number on a strategy, tells me that some patterns in the design, satisfy this specific strategy, and the size of the number, tells me how much.
Here is a picture of a solution the bot made for the star lab. I was asking the bot to get possible solutions to some of the older labs, to get a feeling for how it works. The predicted score was 91%, which is fairly good.
Now comes what worries me. My strategy has a positive score, telling me that the design should be following my strategy.
But the strategy was set to penalize the precence of double AU-pairs. And the design has an overweight of double AU-pairs, so the score should have been negative big time.
Also the strategy states that double AU-pairs are only allowed next to each other in the neck area, if twisted opposite each other. Like this.
I don’t think the strategy is working correct. The bot is slipping too many double AU-pairs through, as my strategy is not stopping them as it is supposed to.
It is the same in a couple of other labs I have checked. It fills in too many AU-pairs compared to what the strategy allows without it being penalized.
Info on the design in question:
Secondary structure: …(((((((…((((((…))))))…((((((…))))))…((((((…))))))…((((((…))))))…)))))))…
Score: 91.28428806268498
Sequence: AAAAAGAAAACCAAAAGGUAACAAAAGUUACCAAAAGUUCGCAAAAGCGAACAAAACAAAAGAAAACUUUUGAAAAGUAUUGAAAACAAUACAAAAGGUUUUCAAAAAAAAAAAAAAAAAAAA
