# \[Strategy Market\] \[Switch\] Elements: Down boost hairpin loops in switching area

**URL:** https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362
**Category:** Strategy Market - Switches
**Created:** [June 16, 2015, 10:26pm UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362 "2015-06-16T22:26:00Z")
**Posts on this page:** 4
**Page:** 1

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### Author: ![Eli\_Fisker](https://forum.eternagame.org/user_avatar/forum.eternagame.org/eli_fisker/32/4453_2.png) [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)
#### Post date: [June 16, 2015, 10:26pm UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362/1 "2015-06-16T22:26:00Z")

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**Strategy**

Penalize end loops that has low energy in loops in hairpins that participate in the switching area.

For hairpin loops in the switching area, at 5 base pair and longer, reward if the end loop has high positive energy and penalize increasingly the more negative the energy becomes.

For hairpin loops in the switching area, at 4 base pairs and shorter, reward up boosting.

**Background**

[![](https://d2he8ud106d9gn.cloudfront.net/original/2X/9/94292f17c43e2ff9abae47b0fbc0eef7e7392554.png)](https://d2r1vs3d9006ap.cloudfront.net/s3_images/1221966/Downboosthairpinloops1.png?1434493336)

[![](https://d2he8ud106d9gn.cloudfront.net/original/2X/6/61153fa5d26b54bcce612121c7fbf133dc8a1bf5.png)](https://d2r1vs3d9006ap.cloudfront.net/s3_images/1221967/Downboosthairpinloops2.png?1434493353)

[https://getsatisfaction.com/eternagam…](https://getsatisfaction.com/eternagame/topics/different_types_of_switches)

[https://docs.google.com/document/d/1f…](https://docs.google.com/document/d/1fj0OeU6nHakAF752OP_U5gcK5KAmtcfps-A_hPJvrPU/edit#bookmark=id.wrp233d3ek9j)

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### Author: ![Brourd](https://forum.eternagame.org/user_avatar/forum.eternagame.org/brourd/32/4408_2.png) [@Brourd](https://forum.eternagame.org/u/Brourd)
#### Post date: [June 16, 2015, 11:47pm UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362/2 "2015-06-16T23:47:00Z")

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I’m not entirely sure that basing this strategy on an observation of a pair of designs with few clusters is valid.

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### Author: ![vineetkosaraju](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/v/4491bb/32.png) [@vineetkosaraju](https://forum.eternagame.org/u/vineetkosaraju)
#### Post date: [June 29, 2015, 7:54pm UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362/3 "2015-06-29T19:54:00Z")

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Dear Eli Fisker,  
&nbsp;  
Your strategy has been added to our implementation queue and we should have it completed within the next two to three weeks. You can check the status of the implementation [here](https://github.com/vineetsk1/Switch-Strategies/issues/23).

We will also be uploading the code used to write your strategy on this [page](https://github.com/vineetsk1/Switch-Strategies) if you are interested in reading it later.

After implementing your idea, we will post the direct link to the code here. Then, we will then optimize the parameters, and test it. At that point, we will tell you the correlation of how good your strategy was and what the new optimized parameters are.

Thanks for sharing your idea!

Vineet Kosaraju  
The EteRNA Team

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### Author: ![vineetkosaraju](https://forum.eternagame.org/letter_avatar_proxy/v4/letter/v/4491bb/32.png) [@vineetkosaraju](https://forum.eternagame.org/u/vineetkosaraju)
#### Post date: [July 7, 2015, 4:25am UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362/4 "2015-07-07T04:25:00Z")

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Dear Eli Fisker,

I am pleased to announce that a preliminary version of your strategy has been implemented with 26 lines of code. The code might slightly change in the future to remove bugs, but you can check the current version [here](https://github.com/vineetsk1/Switch-Strategies/blob/master/eli_fisker_elements_down_boost_hairpin_loops_in_switching_area.py). We will soon work on optimizing your parameters and testing the strategy.

Thank you again for sharing your switch strategy!

Vineet Kosaraju  
The EteRNA Team
