[Strategy market] Legal placement of GU-pairs

Strategy Market Strategy Market - Single State
1

I would like to ad a strategy for placements of GU-pairs

If there is no Gu pair (in the whole design) +2

Gu-pair between two opposite twisted GC-pairs +1 (GC-pairs should be twisted compared to each other)

Gu-pair between 2 GC-pairs where the GC-pairs turn same way compared to each other +0,5

Gu-pair beside one GC-pair +0,5

Gu-pair besides no GC-pair -2

Two GU pairs beside each other, -4, if more -2 pr extra

GU-pair in junction – 1

Neckarea behaves different than the rest of the design, also when it comes to tolerance for GU-pairs, so here I whish for almost double price and half penalty:

If GU-basepair is found in neck:

Gu-pair between two opposite twisted GC-pairs +2

Gu-pair between 2 GC-pairs where the GC-pairs turn same way compared to each other +1

Gu-pair beside one GC-pair +1

Gu-pair besides no GC-pair -1

Two GU pairs beside each other, (turning same way) - one of those are allowed, if more, or the double GU pair are opposite turning, penalize with -2

GU-pair in junction – 0,5

I’m aware that sometimes it seems to matter what way the GU-pair turn compared to the GC-pairs and AU-pairs in it’s surroundings. This strategy is a rough one, that probably will need updating when we have figured out which GU-combinations pays off best. Anyone who have an idea about what these are, is more than welcome to make an improvement of my strategy.

Here is some of the theory behind this:

What’s so special about the neck? part 3

2

Dear Eli,

Your strategy has been added to our implementation queue with task id 43. You can check the schedule of the implementation here.

ETA of the implementation is 7/29/2011

Thanks for sharing your idea!

EteRNA team

3

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 247 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 -0.00373166522865. (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!

4

I’m thinking some of the parts in my strategy are flawed. I propably gave too much points for having GU-pairs in a design, compared to the value of their presence.

I still thinks part of this strategy is still good. So what I wish for, later when funding is no problem, is that the strategy is split up in parts, to see which part of the strategy is useful and to eliminate the bad ones.