[Strategy market] No blue nucleotides in hook area

Strategy Market Strategy Market - Single State
1

I would like to ad a strategy, that says: No blue nucleotides are allowed in the hook area (the nucleotides beside the junctions)

Give -2 for each blue nucleotide in this position

2

Dear Eli,

Your strategy has been added to our implementation queue with task id 27. You can check the schedule of the implementation here.

ETA of the implementation is 6/24/2011

Thanks for sharing your idea!

EteRNA team

3

Hello Eli,

I’m assigned to this strategy as well. This one seems pretty simple so I should be able to get it out rather quickly. I have a few questions for clarification, however:

  • By the hook you mean the nucleotides at the very beginning and end of RNA strands that are not part of stacks, correct? I saw your other post here: http://getsatisfaction.com/eternagame… and I’m pretty sure you mean the nucleotides on the right of the picture you provided that are not part of stacks.

  • What do you mean by “nucleotides beside the junctions”? The way I understood it is you mean to include all nucleotides inside the hook, but do you mean only nucleotides immediately beside the stacks?

Thanks for your help!

4

Hi Jerry!

By hook area I mean this area:

Sorry about the expresion the junctions. I meant the basepair that is closing the area between the neck and hook area. But yes, when I think about it even here I don’t like blue nucleotides. :slight_smile: So no blue nucleotides inside the hook or in the basepair that is connectiong the hook and the neckarea.

Good luck!

5

Thanks for your help Eli! I finished the code and it’s waiting review before being published.

6

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 10 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 0.159745865759. (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!

8

I will add that I now think that blue in the hook (tail) is actually one of the more safer choices, beside A’s. Both the 5’ tail and the 3’ tail should primarily be A’s outside of the tails added for sequencing. (Like the two red GG starting 5’ tail, which are there for getting polymerase to get started.)

But when there are 5 or more single bases in line, 20% of the bases should be other than yellow.

I will like to make a new strategy for the hook and single bases in line:

Below 4 single bases

  • 2 if all is A’s

Above 5+

20% of the bases should be non A’s.

+2 for U’s
+1 for C
0 for red

For each additional non yellow base beyond the 20%, give

-3 for reds
-2 green
-1 blue

If at boost spot, half penalty for red.

I should also add that green Cytosines bases a bit away from the double red Guanines at base 1 and 2, can form a tetraloop with the latter. Which is also unwanted.