# Strategy Market **URL:** https://forum.eternagame.org/c/strategy-market/25.md [Latest](https://forum.eternagame.org/latest.md) · [Categories](https://forum.eternagame.org/categories.md) · [Tags](https://forum.eternagame.org/tags.md) --- ## [About the Strategy Market category](https://forum.eternagame.org/t/about-the-strategy-market-category/3474)
**Author:** [@LFP6](https://forum.eternagame.org/u/LFP6)\ **Replies:** 0\ **Last updated:** [June 26, 2020, 6:19pm UTC](https://forum.eternagame.org/t/about-the-strategy-market-category/3474 "2020-06-26T18:19:43Z")
The strategy market was a feature of early Eterna where players could propose rules for what makes a good RNA design, and Eterna researchers would turn each strategy into code to be scored and integrated into a novel RNA… --- ## [What are the relationships between free energy and the presence of ligands or oligos that bind with an RNA riboswitch?](https://forum.eternagame.org/t/what-are-the-relationships-between-free-energy-and-the-presence-of-ligands-or-oligos-that-bind-with-an-rna-riboswitch/3045)
**Author:** [@IceBolt](https://forum.eternagame.org/u/IceBolt)\ **Replies:** 1\ **Last updated:** [March 25, 2019, 10:09pm UTC](https://forum.eternagame.org/t/what-are-the-relationships-between-free-energy-and-the-presence-of-ligands-or-oligos-that-bind-with-an-rna-riboswitch/3045 "2019-03-25T22:09:00Z")
Hello! I learned that when ligands bind to the RNA, they give the RNA an energy bonus (Decreases free energy) and in the case for oligos, they give the RNA an energy penalty (Increases free energy). I think Ligands give… --- ## [Rapid Process Graph!](https://forum.eternagame.org/t/rapid-process-graph/2973)
**Author:** [@Astromon](https://forum.eternagame.org/u/Astromon)\ **Replies:** 13\ **Last updated:** [October 15, 2018, 3:26am UTC](https://forum.eternagame.org/t/rapid-process-graph/2973 "2018-10-15T03:26:00Z")
Besides the fold change ratio (high being the best) I am not sure what the other things this graph is telling me. Any idea lab players?! --- ## [Area to discuss Switch puzzle analysis and its relation to lab](https://forum.eternagame.org/t/area-to-discuss-switch-puzzle-analysis-and-its-relation-to-lab/2969)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 50\ **Last updated:** [August 25, 2018, 2:24pm UTC](https://forum.eternagame.org/t/area-to-discuss-switch-puzzle-analysis-and-its-relation-to-lab/2969 "2018-08-25T14:24:00Z")
This is a forum area to discuss switch puzzles and their relation to lab. This discussion sprang out of a discussion between Cynwulf and I on switch puzzles that I shared the other day. I put it up at the OpenTB lab whi… --- ## [How to create a ABCCInc puzzle from scratch](https://forum.eternagame.org/t/how-to-create-a-abccinc-puzzle-from-scratch/2925)
**Author:** [@JR1](https://forum.eternagame.org/u/JR1)\ **Replies:** 1\ **Last updated:** [April 30, 2018, 11:53am UTC](https://forum.eternagame.org/t/how-to-create-a-abccinc-puzzle-from-scratch/2925 "2018-04-30T11:53:00Z")
First create a ACInc puzzle around 40 nts in length. The C string will stomp on the A,R strings in the middle. of the A,R strings (seems to be easiest). Avoid kinks and new stems from forming ( again easiest). You can… --- ## [Does RNA naturally want to tangle itself? Thoughts on ideal configurations of switches.](https://forum.eternagame.org/t/does-rna-naturally-want-to-tangle-itself-thoughts-on-ideal-configurations-of-switches/2823)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 11\ **Last updated:** [April 4, 2017, 5:52am UTC](https://forum.eternagame.org/t/does-rna-naturally-want-to-tangle-itself-thoughts-on-ideal-configurations-of-switches/2823 "2017-04-04T05:52:00Z")
Does RNA naturally want to tangel itself? I have been analyzing the OpenTB results and have found that switches tend to like to have a nice long static stem in them and only have other segments switching kinda like a squ… --- ## [About the modeling of binding sites](https://forum.eternagame.org/t/about-the-modeling-of-binding-sites/2791)
**Author:** [@nando](https://forum.eternagame.org/u/nando)\ **Replies:** 0\ **Last updated:** [January 16, 2017, 12:07pm UTC](https://forum.eternagame.org/t/about-the-modeling-of-binding-sites/2791 "2017-01-16T12:07:00Z")
The purpose of this thread is to inform players about the path I took to create the aptamer models and warn them about my ignorance. Let’s take the example of Arginine. The reference structure is deposited on PDB with a… --- ## [\[Strategy Market\] \[Switch\] Kcal difference between states with similar size inputs](https://forum.eternagame.org/t/strategy-market-switch-kcal-difference-between-states-with-similar-size-inputs/2668)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [April 23, 2016, 7:32pm UTC](https://forum.eternagame.org/t/strategy-market-switch-kcal-difference-between-states-with-similar-size-inputs/2668 "2016-04-23T19:32:00Z")
This is a strategy that goes for logic gate labs (state 2 and 3) or labs that have two states where the only difference is a shift of two inputs and the inputs are of similar length. Designs with static stem and lane sh… --- ## [\[Strategy Market-Switch\] DPAT analysis data for R100 for use in designing high and low scoring desings](https://forum.eternagame.org/t/strategy-market-switch-dpat-analysis-data-for-r100-for-use-in-designing-high-and-low-scoring-desings/2635)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 12\ **Last updated:** [March 22, 2016, 1:19am UTC](https://forum.eternagame.org/t/strategy-market-switch-dpat-analysis-data-for-r100-for-use-in-designing-high-and-low-scoring-desings/2635 "2016-03-22T01:19:00Z")
Hi. I just got done running R100 through DPAT and here is all the data it generated through the macro search filter settings for 80-100 scores and 30 60 group scores designs for everyone to use. There are 3 types of file… --- ## [\[Strategy market\] Blue line](https://forum.eternagame.org/t/strategy-market-blue-line/2601)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 5\ **Last updated:** [February 18, 2016, 3:08am UTC](https://forum.eternagame.org/t/strategy-market-blue-line/2601 "2016-02-18T03:08:00Z")
I like to ad a strategy that says, no strands with 3, 4 or more blue nucleotides in line. Penalize for each extra with -1. --- ## [\[Switch Strategy Market\] Ideal FMN MS2 Riboswitches FMN Binding Site Stacks and Minimum Pairing Probabilities](https://forum.eternagame.org/t/switch-strategy-market-ideal-fmn-ms2-riboswitches-fmn-binding-site-stacks-and-minimum-pairing-probabilities/2595)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 2\ **Last updated:** [February 16, 2016, 8:27pm UTC](https://forum.eternagame.org/t/switch-strategy-market-ideal-fmn-ms2-riboswitches-fmn-binding-site-stacks-and-minimum-pairing-probabilities/2595 "2016-02-16T20:27:00Z")
I analyzed FMN MS2 Ribsowitch Round 1 and 2 labs for Exclusion NG 1 (EXNG1), Exclusion NG 2 (EXNG2), Exclusion NG 3 (EXNG3), Same State NG 1 (SSNG1), Same State NG 2 (SSNG2), and Same State NG 3 (SSNG3) by running all t… --- ## [\[Strategy market\] Catalog of necks](https://forum.eternagame.org/t/strategy-market-catalog-of-necks/2586)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 7\ **Last updated:** [January 21, 2016, 11:07pm UTC](https://forum.eternagame.org/t/strategy-market-catalog-of-necks/2586 "2016-01-21T23:07:00Z")
I woke up two days ago with a crazy idea for a strategy. Here it comes: The neckarea is regulary a pain in the neck. I would like a strategy, that re-use necks that is known to work and be highly succesfull. Sort of a c… --- ## [\[Strategy Market\]\[Switch\] Penalize designs with listed stacks for R96 Same State NG 3](https://forum.eternagame.org/t/strategy-market-switch-penalize-designs-with-listed-stacks-for-r96-same-state-ng-3/2527)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [October 9, 2015, 8:14pm UTC](https://forum.eternagame.org/t/strategy-market-switch-penalize-designs-with-listed-stacks-for-r96-same-state-ng-3/2527 "2015-10-09T20:14:00Z")
From DPAT3 penalize designs that have any of the following list of stacks in R96 Same State NG 3 since they are only predicted by Vienna 2 to exist in the MFE structure of poor performing designs only ( designs scoring b… --- ## [\[Strategy Market\]\[Switch\] Penalize designs with listed stacks for R96 Same State NG 2](https://forum.eternagame.org/t/strategy-market-switch-penalize-designs-with-listed-stacks-for-r96-same-state-ng-2/2526)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [October 9, 2015, 8:10pm UTC](https://forum.eternagame.org/t/strategy-market-switch-penalize-designs-with-listed-stacks-for-r96-same-state-ng-2/2526 "2015-10-09T20:10:00Z")
From DPAT3 penalize designs that have any of the following list of stacks in R96 Same State NG 2 since they are only predicted by Vienna 2 to exist in the MFE structure of poor performing designs only ( designs scoring b… --- ## [\[Strategy Market\]\[Switch\] Penalize designs with listed stacks for R96 Same State NG 2](https://forum.eternagame.org/t/strategy-market-switch-penalize-designs-with-listed-stacks-for-r96-same-state-ng-2/2522)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [October 9, 2015, 8:02pm UTC](https://forum.eternagame.org/t/strategy-market-switch-penalize-designs-with-listed-stacks-for-r96-same-state-ng-2/2522 "2015-10-09T20:02:00Z")
From DPAT3 penalize designs that have any of the following list of stacks in R96 Same State NG 2 since they are only predicted by Vienna 2 to exist in the MFE structure of poor performing designs only ( designs scoring b… --- ## [\[Market Strategy\] To MS2 gate or not - Exclusion Labs](https://forum.eternagame.org/t/market-strategy-to-ms2-gate-or-not-exclusion-labs/2516)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 5, 2015, 9:25pm UTC](https://forum.eternagame.org/t/market-strategy-to-ms2-gate-or-not-exclusion-labs/2516 "2015-10-05T21:25:00Z")
Make MS2 gate or not Strategy for easy normal lab. On which FMN to target with the MS2 turnoff sequence or the MS2. Give +4 if the FMN sequence targeted is the one furthest away from the MS2/aptamer turnoff sequence … --- ## [\[Market Strategy\] To MS2 gate or not - Exclusion Labs](https://forum.eternagame.org/t/market-strategy-to-ms2-gate-or-not-exclusion-labs/2515)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 5, 2015, 9:20pm UTC](https://forum.eternagame.org/t/market-strategy-to-ms2-gate-or-not-exclusion-labs/2515 "2015-10-05T21:20:00Z")
Make MS2 gate or not Strategy for easy normal lab. On which FMN to target with the MS2 turnoff sequence or the MS2. Give +4 if the FMN sequence targeted is the one furthest away from the MS2/aptamer turnoff sequence (… --- ## [\[Market Strategy\] Distribute the GU’s](https://forum.eternagame.org/t/market-strategy-distribute-the-gu-s/2514)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 5, 2015, 9:16pm UTC](https://forum.eternagame.org/t/market-strategy-distribute-the-gu-s/2514 "2015-10-05T21:16:00Z")
I think we have GU strategies already, but I think EternaBot distributes a little too much GU and wrongly placed. For easy labs: Give +3 if GU% is 0-5%. Give +1 if GU is 6-10%. Give 0 and start penalize for hig… --- ## [\[Market Strategy\] Multiloop too big - make static stem of excess bases](https://forum.eternagame.org/t/market-strategy-multiloop-too-big-make-static-stem-of-excess-bases/2512)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 5, 2015, 9:07pm UTC](https://forum.eternagame.org/t/market-strategy-multiloop-too-big-make-static-stem-of-excess-bases/2512 "2015-10-05T21:07:00Z")
Turnoff labs (Exclusion) If there are more than 6 single bases in the multiloop ring between the MS2 turnoff and the aptamer gate, penalize exponentially and when EternaBot is designing, throw these excess bases in a st… --- ## [\[Market Strategy\] Aptamer gates are too long](https://forum.eternagame.org/t/market-strategy-aptamer-gates-are-too-long/2510)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 5, 2015, 9:05pm UTC](https://forum.eternagame.org/t/market-strategy-aptamer-gates-are-too-long/2510 "2015-10-05T21:05:00Z")
EternaBot is often making its aptamer gates too long at the end of the aptamer that needs to get moving. I think I can now make a better strategy that covers both Exclusion and Same state labs. Turnoff labs For normal … --- ## [\[Market Strategy\] Color of the MS2/aptamer turnoff sequence](https://forum.eternagame.org/t/market-strategy-color-of-the-ms2-aptamer-turnoff-sequence/2509)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 5, 2015, 8:56pm UTC](https://forum.eternagame.org/t/market-strategy-color-of-the-ms2-aptamer-turnoff-sequence/2509 "2015-10-05T20:56:00Z")
Turnoff lab If the turnoff sequence aims for FMN1 it should be something like UUCC. If it aims for FMN2 it should be something like CCUU. Plus make variations over those themes. Main ingredients are the CC’s. Th… --- ## [\[Market Strategy\] Pressured switch labs](https://forum.eternagame.org/t/market-strategy-pressured-switch-labs/2508)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 5, 2015, 8:51pm UTC](https://forum.eternagame.org/t/market-strategy-pressured-switch-labs/2508 "2015-10-05T20:51:00Z")
Different level hardness of labs, takes different strategies. I think we need a strategy for those labs whose structure forces them to need to go full moving. They can’t be solved with what works for a easy switch. Simi… --- ## [\[Strategy Market\]\[Switch\]Dangeling Tail Ends](https://forum.eternagame.org/t/strategy-market-switch-dangeling-tail-ends/2506)
**Author:** [@salish99](https://forum.eternagame.org/u/salish99)\ **Replies:** 1\ **Last updated:** [October 5, 2015, 7:48am UTC](https://forum.eternagame.org/t/strategy-market-switch-dangeling-tail-ends/2506 "2015-10-05T07:48:00Z")
Dangeling tail ends. It seems to me that having no or only short tails in the 77ish region result in low points: http://prntscr.com/7qumi1 (low scorer) whereas if we have some ample tail there, the points are higher.… --- ## [\[Market strategy\] Penalize GU heavy regions](https://forum.eternagame.org/t/market-strategy-penalize-gu-heavy-regions/2505)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [October 4, 2015, 12:58pm UTC](https://forum.eternagame.org/t/market-strategy-penalize-gu-heavy-regions/2505 "2015-10-04T12:58:00Z")
Strategy For Guanine and Uracil (K) stretches 6+ base of length, begin penalize and penalize exponentially. If there are more such stretches, penalize harshly. Only 1⁄2 penalty if these stretches are in static area an… --- ## [\[Strategy Market\] \[Switch\] Penalize repeat repeat repeats bases](https://forum.eternagame.org/t/strategy-market-switch-penalize-repeat-repeat-repeats-bases/2424)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [July 27, 2015, 12:14am UTC](https://forum.eternagame.org/t/strategy-market-switch-penalize-repeat-repeat-repeats-bases/2424 "2015-07-27T00:14:00Z")
While I’m a big fan of repeats in riboswitches, too much can be too much. Strategy Penalize when there are more than two set of repeat bases in a row. No to penalize: AAUU or CCAA To penalize: AAUUAA or GGCCAA The … --- ## [\[Strategy Market\] \[Switch\] Repeat bases versus cluster count](https://forum.eternagame.org/t/strategy-market-switch-repeat-bases-versus-cluster-count/2423)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [July 27, 2015, 12:12am UTC](https://forum.eternagame.org/t/strategy-market-switch-repeat-bases-versus-cluster-count/2423 "2015-07-27T00:12:00Z")
While I’m a fan of repeat bases in riboswitches, my look at the recent data tells me that too much or too little repeat, seemingly hurts cluster counts. So I decided to hit again with a new strategy. I don’t think my ol… --- ## [\[Strategy Market\] \[Switch\] Cut the blues](https://forum.eternagame.org/t/strategy-market-switch-cut-the-blues/2422)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [July 27, 2015, 12:00am UTC](https://forum.eternagame.org/t/strategy-market-switch-cut-the-blues/2422 "2015-07-27T00:00:00Z")
Strategy Two UU’s in a row are usually no problem. But if they are close like 1 and 2 bases apart, they can be trouble. Start penalizing mildly. Give a small penalty to designs that has 3 UUU’s in a row. Increase p… --- ## [\[Strategy Market\]\[Switch\] closing pair probability](https://forum.eternagame.org/t/strategy-market-switch-closing-pair-probability/2415)
**Author:** [@wuami](https://forum.eternagame.org/u/wuami)\ **Replies:** 0\ **Last updated:** [July 25, 2015, 12:38am UTC](https://forum.eternagame.org/t/strategy-market-switch-closing-pair-probability/2415 "2015-07-25T00:38:00Z")
Ratio of the closing pair probability for on and off states --- ## [Revision 1 - Trend in legs of dotplots in lab "Simple RNA Switch"](https://forum.eternagame.org/t/revision-1-trend-in-legs-of-dotplots-in-lab-simple-rna-switch/2408)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [July 23, 2015, 4:35am UTC](https://forum.eternagame.org/t/revision-1-trend-in-legs-of-dotplots-in-lab-simple-rna-switch/2408 "2015-07-23T04:35:00Z")
Hi Everyone! I posted a thread about a paper I had written analyzing the top 10 and bottom 10 designs from “Simple RNA Switch”. I have just released a 1st revision. I corrected some errors in the tables and graphs as wel… --- ## [\[Strategy Market\] \[Switch\] Static stem in the switching area](https://forum.eternagame.org/t/strategy-market-switch-static-stem-in-the-switching-area/2407)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [July 22, 2015, 8:27pm UTC](https://forum.eternagame.org/t/strategy-market-switch-static-stem-in-the-switching-area/2407 "2015-07-22T20:27:00Z")
The strategy should work for FMN, FMN/MS2 switches and microRNA turnoff switches. Background Strategy Here are a few things that are already made into separate strategies, but are central to this strategy. Reward kno… [Next page](https://forum.eternagame.org/c/strategy-market/25.md?page=1)