# Strategy Market **URL:** https://forum.eternagame.org/c/strategy-market/25.md?page=1 [Latest](https://forum.eternagame.org/latest.md) · [Categories](https://forum.eternagame.org/categories.md) · [Tags](https://forum.eternagame.org/tags.md) **Page:** 2 --- ## [Strategy Market\] \[Switch\] Award Multiloops in FMN/MS2 Switches](https://forum.eternagame.org/t/strategy-market-switch-award-multiloops-in-fmn-ms2-switches/2406)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [July 22, 2015, 7:29pm UTC](https://forum.eternagame.org/t/strategy-market-switch-award-multiloops-in-fmn-ms2-switches/2406 "2015-07-22T19:29:00Z")
Strategy Give +2 if there is a multiloop in state 1 and Give +2 if there is a multiloop in state 2 Give additional +4 if there is a multiloop in both states The multiloop should be part of the switching area … --- ## [\[Strategy Market\]\[Switch\] Award high pairing probability of hairpin forming per dotplot](https://forum.eternagame.org/t/strategy-market-switch-award-high-pairing-probability-of-hairpin-forming-per-dotplot/2400)
**Author:** [@Jennifer\_Pearl](https://forum.eternagame.org/u/Jennifer_Pearl)\ **Replies:** 0\ **Last updated:** [July 19, 2015, 11:50pm UTC](https://forum.eternagame.org/t/strategy-market-switch-award-high-pairing-probability-of-hairpin-forming-per-dotplot/2400 "2015-07-19T23:50:00Z")
I think based on my analysis of the lab “Simple RNA Switch” that if the switch is from one hairpin on a base loop to another hairpin on a base loop with an aptamer in the middle in the 2nd state the hairpin before the ap… --- ## [\[Strategy Market\] \[Switch\] FMN1 versus FMN2](https://forum.eternagame.org/t/strategy-market-switch-fmn1-versus-fmn2/2388)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [July 13, 2015, 6:33pm UTC](https://forum.eternagame.org/t/strategy-market-switch-fmn1-versus-fmn2/2388 "2015-07-13T18:33:00Z")
Strategy for MS2/FMN labs Turnoff labs Give +2 for each base, if the FMN sequence involved in the switching is the one closest to the MS2 sequence Give +4 for each base, if the FMN sequence involved in the switchi… --- ## [\[Strategy Market\] \[Switch\] Complementary word change game - MicroRNA Turn on lab](https://forum.eternagame.org/t/strategy-market-switch-complementary-word-change-game-microrna-turn-on-lab/2383)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 7\ **Last updated:** [July 10, 2015, 4:28pm UTC](https://forum.eternagame.org/t/strategy-market-switch-complementary-word-change-game-microrna-turn-on-lab/2383 "2015-07-10T16:28:00Z")
Strategy Intro Strategy courtesy to jandersonlee because of pattern origin. Strategy: MicroRNA turn on lab Give +3 for each base in stretch 2 that is strongly complementary to stretch 1 (particular stretch in microRNA… --- ## [\[Strategy Market\]\[Switch\] kinks](https://forum.eternagame.org/t/strategy-market-switch-kinks/2380)
**Author:** [@JR1](https://forum.eternagame.org/u/JR1)\ **Replies:** 4\ **Last updated:** [July 9, 2015, 11:23pm UTC](https://forum.eternagame.org/t/strategy-market-switch-kinks/2380 "2015-07-09T23:23:00Z")
1.) high energy positive kink in stack that contains misformed ligend in state 1 stack OK if ligend to be formed in state 2 Plus if kink exists in correct stack 2.) kink in state 1 stack OK where stack splits into inte… --- ## [\[Strategy Market\]\[Switch\] Strategy](https://forum.eternagame.org/t/strategy-market-switch-strategy/2379)
**Author:** [@JR1](https://forum.eternagame.org/u/JR1)\ **Replies:** 4\ **Last updated:** [July 9, 2015, 10:54pm UTC](https://forum.eternagame.org/t/strategy-market-switch-strategy/2379 "2015-07-09T22:54:00Z")
1.) 3 stacks max. , 2 better penalize if more than 3 stacks 2.) half of sequence in invariant when folding between states penalize if entire sequence is folding strong penalty if is 3 dimensional (it looks like twis… --- ## [\[Strategy Market\] \[Switch\] Obligate switching bases versus additional switching bases](https://forum.eternagame.org/t/strategy-market-switch-obligate-switching-bases-versus-additional-switching-bases/2378)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 9, 2015, 5:44pm UTC](https://forum.eternagame.org/t/strategy-market-switch-obligate-switching-bases-versus-additional-switching-bases/2378 "2015-07-09T17:44:00Z")
I got inspired from the discussion with Omei and Vineet. (See the Strategy on obligate switching base pairs) So I made a new strategy. :slight\_smile: Strategy Intro Generally I think it smarter to lock up areas of a sw… --- ## [\[Strategy Market\] \[Switch\] Complementary Zipper Style - MS2/FMN Turnon labs](https://forum.eternagame.org/t/strategy-market-switch-complementary-zipper-style-ms2-fmn-turnon-labs/2377)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 9, 2015, 5:13pm UTC](https://forum.eternagame.org/t/strategy-market-switch-complementary-zipper-style-ms2-fmn-turnon-labs/2377 "2015-07-09T17:13:00Z")
Strategy Intro This strategy is in courtesy of Nando and Brourd. Nando for his explanations of RNA switch zipping and Brourd for origin of pattern. I noticed that a specific part of the MS2 hairpin stem very often gets… --- ## [\[Strategy Market\] \[Switch\] Elements: Obligatory switching base pairs in MS2/FMN switches](https://forum.eternagame.org/t/strategy-market-switch-elements-obligatory-switching-base-pairs-in-ms2-fmn-switches/2375)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 14\ **Last updated:** [July 8, 2015, 4:37pm UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-obligatory-switching-base-pairs-in-ms2-fmn-switches/2375 "2015-07-08T16:37:00Z")
Intro As a rule of thumb the obligate switching base pairs in a MS2/FMN switch are following: The 3 base pairs after the switching end of the aptamer are mandatory, since they needs to be filled to make a legal solve… --- ## [\[Strategy Market\] \[Switch\] JL’s microRNA fish hook 2: MicroRNA landing spots](https://forum.eternagame.org/t/strategy-market-switch-jl-s-microrna-fish-hook-2-microrna-landing-spots/2372)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 8, 2015, 3:39pm UTC](https://forum.eternagame.org/t/strategy-market-switch-jl-s-microrna-fish-hook-2-microrna-landing-spots/2372 "2015-07-08T15:39:00Z")
Intro This strategy is courtesy to jandersonlee and based on his superior round 1 microRNA design strategy, that ended hitting through among the majority of the winners in the following round too. Strategy for Turn on … --- ## [\[Strategy Market\] \[Switch\] JL’s microRNA fish hook 1](https://forum.eternagame.org/t/strategy-market-switch-jl-s-microrna-fish-hook-1/2369)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 4\ **Last updated:** [July 8, 2015, 6:32am UTC](https://forum.eternagame.org/t/strategy-market-switch-jl-s-microrna-fish-hook-1/2369 "2015-07-08T06:32:00Z")
Intro This strategy is courtesy to jandersonlee and based on his superior round 1 microRNA design strategy, that ended hitting through among the majority of the winners in the following round too. Strategy for micro… --- ## [\[Strategy Market\] \[Switch\] Elements: How to turn off MS2](https://forum.eternagame.org/t/strategy-market-switch-elements-how-to-turn-off-ms2/2367)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 8, 2015, 4:43am UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-how-to-turn-off-ms2/2367 "2015-07-08T04:43:00Z")
Intro I mentioned that EternaBot didn’t always had an idea of which elements in the RNA designs are important and why. How to turn off MS2 effectively is one of them. Strategy for turnoff labs Reward designs where M… --- ## [\[Strategy Market\] \[Switch\] Elements: When to make the tails pair](https://forum.eternagame.org/t/strategy-market-switch-elements-when-to-make-the-tails-pair/2366)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 9\ **Last updated:** [July 7, 2015, 9:13pm UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-when-to-make-the-tails-pair/2366 "2015-07-07T21:13:00Z")
Intro I mentioned that EternaBot didn’t always had an idea of what parts to pair up and when. Tails are one of them. Strategy for tail ends Distance to next element from both ends of the sequence: For 11 bases or mor… --- ## [\[Strategy Market\] \[Switch\] Elements: MS2 Gates](https://forum.eternagame.org/t/strategy-market-switch-elements-ms2-gates/2365)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 7, 2015, 6:09am UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-ms2-gates/2365 "2015-07-07T06:09:00Z")
Strategy for Exclusion labs (Turnoff labs) Give 3+ if there is a 2 base pair stack forming close in front of the MS2 when it is forming. That stack in front of the MS2 is what I call MS2 gate. Give 2+ if there is a 3 b… --- ## [\[Strategy Market\] \[Switch\] Element: Aptamer Gate](https://forum.eternagame.org/t/strategy-market-switch-element-aptamer-gate/2364)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 7, 2015, 5:34am UTC](https://forum.eternagame.org/t/strategy-market-switch-element-aptamer-gate/2364 "2015-07-07T05:34:00Z")
What eternabot doesn’t know - yet I was looking at some of the eternabot strategies that were uploaded before last round closed. And I thought to myself, the bot is all over the place. Because it has no idea what elemen… --- ## [\[Strategy Market\] \[Switch\] Element: Distance between MS2 and aptamer sequences](https://forum.eternagame.org/t/strategy-market-switch-element-distance-between-ms2-and-aptamer-sequences/2363)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 7, 2015, 5:12am UTC](https://forum.eternagame.org/t/strategy-market-switch-element-distance-between-ms2-and-aptamer-sequences/2363 "2015-07-07T05:12:00Z")
Strategy for turn on labs (Same State) For when MS2 sequence is in between the FMN sequences Give bonus if there are 11 single bases or less at the shortest side between the aptamer on either side and the MS2 sequence.… --- ## [\[Strategy Market\] \[Switch\] Elements: Down boost hairpin loops in switching area](https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 3\ **Last updated:** [July 7, 2015, 4:25am UTC](https://forum.eternagame.org/t/strategy-market-switch-elements-down-boost-hairpin-loops-in-switching-area/2362 "2015-07-07T04:25:00Z")
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 … --- ## [\[Strategy Market\]\[Switch\] Use MS2 arm bases in closing stem for FMN aptamer](https://forum.eternagame.org/t/strategy-market-switch-use-ms2-arm-bases-in-closing-stem-for-fmn-aptamer/2361)
**Author:** [@jandersonlee](https://forum.eternagame.org/u/jandersonlee)\ **Replies:** 2\ **Last updated:** [July 7, 2015, 3:33am UTC](https://forum.eternagame.org/t/strategy-market-switch-use-ms2-arm-bases-in-closing-stem-for-fmn-aptamer/2361 "2015-07-07T03:33:00Z")
For an exclusion switch involving FMN and MS2, reward designs that include some of the MS2 binding arm in at least one on the closing stems on the FMN aptamer loop. Give higher reward for more bases used, up to 5. --- ## [\[Strategy Market\]\[Switch\]A guidance](https://forum.eternagame.org/t/strategy-market-switch-a-guidance/2358)
**Author:** [@salish99](https://forum.eternagame.org/u/salish99)\ **Replies:** 4\ **Last updated:** [July 6, 2015, 5:58pm UTC](https://forum.eternagame.org/t/strategy-market-switch-a-guidance/2358 "2015-07-06T17:58:00Z")
For increasingyiled in the mirna fast result puzzles (Johan’s lab) we discussed intensively to limit the number of A’s. This has already been implemented by the A-dometer. Furthermore, it was shown in our tables that … --- ## [\[Strategy Market\] \[Switch\] How MicroRNA likes to bind: Turn on labs](https://forum.eternagame.org/t/strategy-market-switch-how-microrna-likes-to-bind-turn-on-labs/2356)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 6, 2015, 5:15pm UTC](https://forum.eternagame.org/t/strategy-market-switch-how-microrna-likes-to-bind-turn-on-labs/2356 "2015-07-06T17:15:00Z")
Intro It is not just switches that are different from static designs, also switches involving microRNA are different from the regular MS2/aptamer switch designs. Therefore a specific strategy for turnon microRNA labs. S… --- ## [\[Strategy Market\] \[Switch\] How MicroRNA likes to bind: Turnoff labs](https://forum.eternagame.org/t/strategy-market-switch-how-microrna-likes-to-bind-turnoff-labs/2354)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 6, 2015, 4:32pm UTC](https://forum.eternagame.org/t/strategy-market-switch-how-microrna-likes-to-bind-turnoff-labs/2354 "2015-07-06T16:32:00Z")
Intro It is not just switches that are different from static designs, also microRNA labs wants different things depending if they belong to the turn on or turnoff variant. :slight\_smile: Therefore a specific strategy fo… --- ## [\[Strategy Market\] \[Switch\] Helix Composition](https://forum.eternagame.org/t/strategy-market-switch-helix-composition/2352)
**Author:** [@Brourd](https://forum.eternagame.org/u/Brourd)\ **Replies:** 2\ **Last updated:** [July 5, 2015, 11:30pm UTC](https://forum.eternagame.org/t/strategy-market-switch-helix-composition/2352 "2015-07-05T23:30:00Z")
First, we’ll define a helix with this particular strategy as being a continuous series of consecutive base pairs. For now, all loops will terminate a helix. Second, let’s separate the helices into classes. Active helic… --- ## [\[Strategy Market\]\[Switch\] Shape stable against mutation](https://forum.eternagame.org/t/strategy-market-switch-shape-stable-against-mutation/2351)
**Author:** [@jandersonlee](https://forum.eternagame.org/u/jandersonlee)\ **Replies:** 5\ **Last updated:** [July 5, 2015, 10:35pm UTC](https://forum.eternagame.org/t/strategy-market-switch-shape-stable-against-mutation/2351 "2015-07-05T22:35:00Z")
For all pairs that bond the same way in both on and off modes, subtract one point for each pair that when flipped causes the secondary structure to change in either mode and two points if it causes the secondary structur… --- ## [\[Strategy Market\]\[Switch\] Fix one Stem of FMN Aptamer loop](https://forum.eternagame.org/t/strategy-market-switch-fix-one-stem-of-fmn-aptamer-loop/2350)
**Author:** [@jandersonlee](https://forum.eternagame.org/u/jandersonlee)\ **Replies:** 8\ **Last updated:** [July 5, 2015, 8:06pm UTC](https://forum.eternagame.org/t/strategy-market-switch-fix-one-stem-of-fmn-aptamer-loop/2350 "2015-07-05T20:06:00Z")
For an FMN switch, reward designs that keep one of the two closing stems fixed (i.e paired the same way) in both states of the switch. --- ## [\[Strategy Market\] \[Switch\]](https://forum.eternagame.org/t/strategy-market-switch/2349)
**Author:** [@wateronthemoon](https://forum.eternagame.org/u/wateronthemoon)\ **Replies:** 2\ **Last updated:** [July 5, 2015, 7:17pm UTC](https://forum.eternagame.org/t/strategy-market-switch/2349 "2015-07-05T19:17:00Z")
Try GU. For example, if you have a loop that should remain open in one state and pair into a stack in the other, often GU can be valuable (strong enough to bind, weak enough to come apart). That’s my 2 cents. --- ## [\[Strategy Market\] \[Switch\] Entropy in MS2/microRNA designs](https://forum.eternagame.org/t/strategy-market-switch-entropy-in-ms2-microrna-designs/2347)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 4\ **Last updated:** [July 5, 2015, 5:24pm UTC](https://forum.eternagame.org/t/strategy-market-switch-entropy-in-ms2-microrna-designs/2347 "2015-07-05T17:24:00Z")
Strategy Give -1 for designs having lower than 0.6 in entropy and penalize exponentially Give +1 for designs having above 0.6-0.8 in entropy Give +3 to designs having between 0.9-1.5 in entropy Give +1 to designs tha… --- ## [\[Strategy Market\] \[Switch\] Entropy in MS2/aptamer switches](https://forum.eternagame.org/t/strategy-market-switch-entropy-in-ms2-aptamer-switches/2344)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 7\ **Last updated:** [July 4, 2015, 9:44pm UTC](https://forum.eternagame.org/t/strategy-market-switch-entropy-in-ms2-aptamer-switches/2344 "2015-07-04T21:44:00Z")
Intro While I was working on making my entropy/switch strategy more specific, I started wondering. Do turnoff labs have higher entropy than turnon labs? And it really seems to be the case. So I’m splitting strategies af… --- ## [\[Strategy Market\]\[Switch\] Energy Model Agnostic](https://forum.eternagame.org/t/strategy-market-switch-energy-model-agnostic/2343)
**Author:** [@jandersonlee](https://forum.eternagame.org/u/jandersonlee)\ **Replies:** 2\ **Last updated:** [July 4, 2015, 8:44pm UTC](https://forum.eternagame.org/t/strategy-market-switch-energy-model-agnostic/2343 "2015-07-04T20:44:00Z")
Reward designs that fold similarly in both energy models in each switch state. Deduct points for the percentage of bonded pairs that differs in each state between energy models. --- ## [\[Strategy Market\] \[Switch\] Entropy in static area in partial switch](https://forum.eternagame.org/t/strategy-market-switch-entropy-in-static-area-in-partial-switch/2340)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 4, 2015, 6:30pm UTC](https://forum.eternagame.org/t/strategy-market-switch-entropy-in-static-area-in-partial-switch/2340 "2015-07-04T18:30:00Z")
Strategy For partial switches: Give 2+ if the non switching area has below 0.7 in entropy Give 1+ if the non switching area has 0.8-0.9 in entropy Give -1 and penalize exponentially, the higher the entropy gets above… --- ## [\[Strategy Market\]\[Switch\] Minimal change](https://forum.eternagame.org/t/strategy-market-switch-minimal-change/2338)
**Author:** [@jandersonlee](https://forum.eternagame.org/u/jandersonlee)\ **Replies:** 2\ **Last updated:** [July 4, 2015, 5:24pm UTC](https://forum.eternagame.org/t/strategy-market-switch-minimal-change/2338 "2015-07-04T17:24:00Z")
Reward switches that have more common structure pairs between the two states. [Previous page](https://forum.eternagame.org/c/strategy-market/25.md) [Next page](https://forum.eternagame.org/c/strategy-market/25.md?page=2)