# Strategy Market **URL:** https://forum.eternagame.org/c/strategy-market/25.md?page=2 [Latest](https://forum.eternagame.org/latest.md) · [Categories](https://forum.eternagame.org/categories.md) · [Tags](https://forum.eternagame.org/tags.md) **Page:** 3 --- ## [\[Strategy Market\] \[Switch\] Dot plot](https://forum.eternagame.org/t/strategy-market-switch-dot-plot/2337)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [July 3, 2015, 10:44pm UTC](https://forum.eternagame.org/t/strategy-market-switch-dot-plot/2337 "2015-07-03T22:44:00Z")
There was a a past strategy with cleanness of dot plot for static designs. The first switch lab we made, many designs had ugly and messy dot plots. But for our MS2 switches, the trend is going towards surprisingly clean … --- ## [\[Strategy Market\]\[Switch\]Predicted probability of MS2 hairpin fully forming](https://forum.eternagame.org/t/strategy-market-switch-predicted-probability-of-ms2-hairpin-fully-forming/2336)
**Author:** [@Omei](https://forum.eternagame.org/u/Omei)\ **Replies:** 2\ **Last updated:** [July 3, 2015, 9:50pm UTC](https://forum.eternagame.org/t/strategy-market-switch-predicted-probability-of-ms2-hairpin-fully-forming/2336 "2015-07-03T21:50:00Z")
From the dot plots produced by ViennaFold 2.2 for the ON and OFF state, pull the probability of the pair forming at the base of MS2 hairpin. Here’s a picture to illustrate the pair, but the exact base numbers will depend… --- ## [\[Strategy Market\]\[Switch\]Dot Plot](https://forum.eternagame.org/t/strategy-market-switch-dot-plot/2330)
**Author:** [@salish99](https://forum.eternagame.org/u/salish99)\ **Replies:** 2\ **Last updated:** [July 1, 2015, 4:56pm UTC](https://forum.eternagame.org/t/strategy-market-switch-dot-plot/2330 "2015-07-01T16:56:00Z")
see https://getsatisfaction.com/eternagam… --- ## [\[Strategy Market\]\[Switch\]Base Pair limits](https://forum.eternagame.org/t/strategy-market-switch-base-pair-limits/2328)
**Author:** [@salish99](https://forum.eternagame.org/u/salish99)\ **Replies:** 2\ **Last updated:** [June 30, 2015, 11:02pm UTC](https://forum.eternagame.org/t/strategy-market-switch-base-pair-limits/2328 "2015-06-30T23:02:00Z")
In accordance with https://getsatisfaction.com/eternagam… AND knowing that the data we have from the phosphorescence labs does not represent shape data, merely what eterna in Vienna 1 thinks the likeliest shape could b… --- ## [\[Strategy Market\] \[Switch\] Base pair difference between states for MS2/FMN switches](https://forum.eternagame.org/t/strategy-market-switch-base-pair-difference-between-states-for-ms2-fmn-switches/2327)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [June 30, 2015, 10:10pm UTC](https://forum.eternagame.org/t/strategy-market-switch-base-pair-difference-between-states-for-ms2-fmn-switches/2327 "2015-06-30T22:10:00Z")
Intro Another thing that matters a great deal for how easy it is to make a switch switch well, is that there isn’t too big a difference in the amount of base pairs per state. Switch designs that have a very big differe… --- ## [\[Strategy Market\] \[Switch\] Penalize long stems in switching area](https://forum.eternagame.org/t/strategy-market-switch-penalize-long-stems-in-switching-area/2325)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [June 30, 2015, 9:41pm UTC](https://forum.eternagame.org/t/strategy-market-switch-penalize-long-stems-in-switching-area/2325 "2015-06-30T21:41:00Z")
Intro As soon as stems in the switching area becomes long, switching becomes harder. I think, as a rough estimate that stems the size of 7 bp and above are generally counterproductive for switching. MicroRNA Strategy P… --- ## [\[Strategy Market\] \[Switch\] Base relationship between non repeat bases](https://forum.eternagame.org/t/strategy-market-switch-base-relationship-between-non-repeat-bases/2323)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [June 30, 2015, 8:55pm UTC](https://forum.eternagame.org/t/strategy-market-switch-base-relationship-between-non-repeat-bases/2323 "2015-06-30T20:55:00Z")
Intro As I were looking repeat bases in top scoring switch designs, I noticed that there seemed to be a relation between amount of single bases in relation to each other. There generally were more single A’s than single… --- ## [\[Strategy Market\] \[Switch\] Amount of repeat bases](https://forum.eternagame.org/t/strategy-market-switch-amount-of-repeat-bases/2322)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [June 29, 2015, 11:49pm UTC](https://forum.eternagame.org/t/strategy-market-switch-amount-of-repeat-bases/2322 "2015-06-29T23:49:00Z")
Intro There seemingly is a difference in amount of repeats, between Turn on labs (same state) versus Turnoff labs (exclusion). So I have made strategies that aims to reward designs with a good percentage of base repeats… --- ## [\[Strategy Market\] \[Switch\] Percentages of A’s.](https://forum.eternagame.org/t/strategy-market-switch-percentages-of-a-s/2321)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [June 29, 2015, 9:50pm UTC](https://forum.eternagame.org/t/strategy-market-switch-percentages-of-a-s/2321 "2015-06-29T21:50:00Z")
Intro Here is a strategy that aims to reward good A percentage levels. EternaBot already gets in a good range most of the time. Thumbs up! :slight\_smile: But I think this could improve it a bit. Strategy A’s percentag… --- ## [\[Strategy Market\]\[Switch\]Base limits](https://forum.eternagame.org/t/strategy-market-switch-base-limits/2320)
**Author:** [@salish99](https://forum.eternagame.org/u/salish99)\ **Replies:** 11\ **Last updated:** [June 29, 2015, 9:29pm UTC](https://forum.eternagame.org/t/strategy-market-switch-base-limits/2320 "2015-06-29T21:29:00Z")
Thsi may already have been implemented. In accordance with https://getsatisfaction.com/eternagam… To achieve high binding energies, we need: a) 10-15% C b) 35-60 % A c) 10-16 % U d) 35 % G for Ex3, and 12-16 % G … --- ## [\[Strategy Market\]\[Switch\] Penalize large amounts of GC pairs](https://forum.eternagame.org/t/strategy-market-switch-penalize-large-amounts-of-gc-pairs/2319)
**Author:** [@vineetkosaraju](https://forum.eternagame.org/u/vineetkosaraju)\ **Replies:** 4\ **Last updated:** [June 29, 2015, 7:31pm UTC](https://forum.eternagame.org/t/strategy-market-switch-penalize-large-amounts-of-gc-pairs/2319 "2015-06-29T19:31:00Z")
Note: This is an example of strategy submission in the EteRNA Strategy Market My strategy is to look at the percentage of GC pairs in the design. I think that a large number of GC pairs would prevent the secondary struc… --- ## [\[Strategy Market\] GU's in barcode](https://forum.eternagame.org/t/strategy-market-gus-in-barcode/2188)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 5\ **Last updated:** [September 24, 2014, 7:04pm UTC](https://forum.eternagame.org/t/strategy-market-gus-in-barcode/2188 "2014-09-24T19:04:00Z")
I noticed that designs with long stems that had a GU in the barcode often looked stabler than their counterparts without it. I will like this strategy: In designs with with one or more stems of the length 8-9+ basepairs… --- ## [\[Market Strategy\] GU Flip Strategy](https://forum.eternagame.org/t/market-strategy-gu-flip-strategy/2087)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [March 26, 2014, 12:11am UTC](https://forum.eternagame.org/t/market-strategy-gu-flip-strategy/2087 "2014-03-26T00:11:00Z")
Read about background idea \[here\](https://getsatisfaction.com/eternagame/topics /gu\_motif#reply\_14053794). --- ## [\[Market Strategy\] GU and AU orientation](https://forum.eternagame.org/t/market-strategy-gu-and-au-orientation/2085)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [March 25, 2014, 11:54pm UTC](https://forum.eternagame.org/t/market-strategy-gu-and-au-orientation/2085 "2014-03-25T23:54:00Z")
I would like a strategy that says: 2 if purine (R) (Guanine and Adenine) is to the right 1 if pyrimidine (Y) (Cytosine and Uracil) is to the right Idea background here. This is for multiloops, in case the closing bas… --- ## [\[Strategy market\] Tetraloop similarity](https://forum.eternagame.org/t/strategy-market-tetraloop-similarity/2082)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 8\ **Last updated:** [March 18, 2014, 6:14pm UTC](https://forum.eternagame.org/t/strategy-market-tetraloop-similarity/2082 "2014-03-18T18:14:00Z")
I would like a strategy that ad points for having similar energy content in tetraloops (like quardruplet) as best, double twin tetraloops as next best. For designs with 4 tetraloops: If all tetraloops are similar in en… --- ## [\[Strategy market\] Bad hook](https://forum.eternagame.org/t/strategy-market-bad-hook/2074)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [March 12, 2014, 7:41pm UTC](https://forum.eternagame.org/t/strategy-market-bad-hook/2074 "2014-03-12T19:41:00Z")
The closer a red base is to the 2 GG’s (base 1 and 2), the worse. I think that having other colored bases than yellow on 5’ tail part, closer to the starting GG’s is worse than if they are more distanced. I have regularl… --- ## [\[Strategy market\] No blue nucleotides in hook area](https://forum.eternagame.org/t/strategy-market-no-blue-nucleotides-in-hook-area/2073)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 7\ **Last updated:** [March 12, 2014, 7:33pm UTC](https://forum.eternagame.org/t/strategy-market-no-blue-nucleotides-in-hook-area/2073 "2014-03-12T19:33:00Z")
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 --- ## [\[Strategy Market\] Use a double G on a single-basepair bulge](https://forum.eternagame.org/t/strategy-market-use-a-double-g-on-a-single-basepair-bulge/2064)
**Author:** [@salish99](https://forum.eternagame.org/u/salish99)\ **Replies:** 7\ **Last updated:** [March 6, 2014, 5:09pm UTC](https://forum.eternagame.org/t/strategy-market-use-a-double-g-on-a-single-basepair-bulge/2064 "2014-03-06T17:09:00Z")
Of the 24 possibilities of base pairs in a single base pair bulge, the G-G combination results in a -0.4J free energy, the lowest of the choices, acting with a significant attractive force without actually bonding. So, … --- ## [\[Strategy Market\] Add a red to each ring](https://forum.eternagame.org/t/strategy-market-add-a-red-to-each-ring/2052)
**Author:** [@salish99](https://forum.eternagame.org/u/salish99)\ **Replies:** 0\ **Last updated:** [February 15, 2014, 9:05pm UTC](https://forum.eternagame.org/t/strategy-market-add-a-red-to-each-ring/2052 "2014-02-15T21:05:00Z")
I suggest after adding a +1 when adding one red (G) to each ring and bulge (note that I don’t suggest a +1 for each added G, just on the overall structure), at the attachment of each hairpin - if there is a choice. One… --- ## [\[Market Strategy\] GU motif](https://forum.eternagame.org/t/market-strategy-gu-motif/2045)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 0\ **Last updated:** [February 7, 2014, 2:11pm UTC](https://forum.eternagame.org/t/market-strategy-gu-motif/2045 "2014-02-07T14:11:00Z")
General Give -2 if motif is 2 basepair or closer to closing basepair. Give -1 if motif starts in closing basepair Give + 2 for motif in stems in stems 7 bp and longer. Give + 1 if open base is complementary to moti… --- ## [\[ Strategy Market \] Stem Structure](https://forum.eternagame.org/t/strategy-market-stem-structure/2044)
**Author:** [@Valareos](https://forum.eternagame.org/u/Valareos)\ **Replies:** 1\ **Last updated:** [February 6, 2014, 8:26pm UTC](https://forum.eternagame.org/t/strategy-market-stem-structure/2044 "2014-02-06T20:26:00Z")
Hope you still receiving submissions for this. used this strategy for building in puzzles and have had a LOT of luck in solving them with this method, so Im curious how it stacks up. Bond Pairs at end of Stems: GC or CG … --- ## [\[Strategy market\] Numbers of yellow nucleotides pr. length of string](https://forum.eternagame.org/t/strategy-market-numbers-of-yellow-nucleotides-pr-length-of-string/2019)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 3\ **Last updated:** [January 10, 2014, 6:17pm UTC](https://forum.eternagame.org/t/strategy-market-numbers-of-yellow-nucleotides-pr-length-of-string/2019 "2014-01-10T18:17:00Z")
I would like to ad a strategy for numbers of yellow nucleotides allowed pr. lengt of string (neckarea excluded): If a string/arm is this number of nucleotides long, then allow this number of yellow adenine. For each yel… --- ## [\[Strategy Market\] Stacks should be made of 10% of GU pairs](https://forum.eternagame.org/t/strategy-market-stacks-should-be-made-of-10-of-gu-pairs/2017)
**Author:** [@sombra0666](https://forum.eternagame.org/u/sombra0666)\ **Replies:** 0\ **Last updated:** [January 4, 2014, 3:06am UTC](https://forum.eternagame.org/t/strategy-market-stacks-should-be-made-of-10-of-gu-pairs/2017 "2014-01-04T03:06:00Z")
(sorry for my english, i’m not from USA) Making too much of GC or AU pairs is never good, right? So i thought that maybe there should be a minimum value for the weak pairs, and that minimum quantity could, somehow, make … --- ## [\[Strategy Market\] Eternacac'c Berex Revisited](https://forum.eternagame.org/t/strategy-market-eternacacc-berex-revisited/2006)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 1\ **Last updated:** [December 21, 2013, 7:12am UTC](https://forum.eternagame.org/t/strategy-market-eternacacc-berex-revisited/2006 "2013-12-21T07:12:00Z")
Gross Berex Ratio = GBR = (Non\_AU)/AU = (ideal)55/45 & both numerator & denominator are fib or sums of fib numbers. 1,1,2,3,5,8,13,21,44,65…Total Nt’s = sum of four fib numbers,i.e., 100=(21+21+13+(44+1)) each nt-group… --- ## [\[Market strategy\] Direction of GC-pairs in small and big multiloops (symmetric)](https://forum.eternagame.org/t/market-strategy-direction-of-gc-pairs-in-small-and-big-multiloops-symmetric/2005)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 2\ **Last updated:** [December 19, 2013, 1:58pm UTC](https://forum.eternagame.org/t/market-strategy-direction-of-gc-pairs-in-small-and-big-multiloops-symmetric/2005 "2013-12-19T13:58:00Z")
I would like to ad a strategy about size of multiloop Symmetic multiloop = multiloop with same numbers of nucleotides between the multiloop arms. Here is my hypothesis: Tolerance for opposite direction of GC-pairs in a… --- ## [\[Market strategy\] GU's in long stems](https://forum.eternagame.org/t/market-strategy-gus-in-long-stems/1997)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 3\ **Last updated:** [December 3, 2013, 11:46am UTC](https://forum.eternagame.org/t/market-strategy-gus-in-long-stems/1997 "2013-12-03T11:46:00Z")
Give +1 if a stem at the length of 8+ contains a GU-basepair at least 2 basepairs away from the closing basepairs. For every additional +7 basepairs a stem is long give +1 if there is another GU basepair. Background: h… --- ## [\[Strategy Market\] Stack Pair Fibonacci Ratios](https://forum.eternagame.org/t/strategy-market-stack-pair-fibonacci-ratios/1899)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 0\ **Last updated:** [September 23, 2013, 4:10pm UTC](https://forum.eternagame.org/t/strategy-market-stack-pair-fibonacci-ratios/1899 "2013-09-23T16:10:00Z")
Strategy Market idea: A pairwise ratio between total stack pairs must approximate a fibonacci ratio so that any pair approaches a fib ratio with another pair. Closer to whole number fib ratio scores higher. Might order … --- ## [\[Strategy Market\] Strictly Alternating Nt's](https://forum.eternagame.org/t/strategy-market-strictly-alternating-nts/1898)
**Author:** [@eternacac](https://forum.eternagame.org/u/eternacac)\ **Replies:** 0\ **Last updated:** [September 23, 2013, 3:33pm UTC](https://forum.eternagame.org/t/strategy-market-strictly-alternating-nts/1898 "2013-09-23T15:33:00Z")
Stack nt’s of each non-A type (U,G,C) should be strictly alternating from 3’ to 5’ to 3’ etc. as you follow down the stack. Penalize each repeated violation in an exponential manner if they are in adjacent base pairs, li… --- ## [\[Market strategy\] Direction of GC-pairs in asymmetric multiloops](https://forum.eternagame.org/t/market-strategy-direction-of-gc-pairs-in-asymmetric-multiloops/865)
**Author:** [@Eli\_Fisker](https://forum.eternagame.org/u/Eli_Fisker)\ **Replies:** 3\ **Last updated:** [August 11, 2013, 12:54pm UTC](https://forum.eternagame.org/t/market-strategy-direction-of-gc-pairs-in-asymmetric-multiloops/865 "2013-08-11T12:54:00Z")
Asymmetic multiloop = multiloop with different numbers of nucleotides between the multiloop arms. I would like a strategy for designs with asymmetric multiloop. Hypothesis: the shorter between GC-pairs in multiloops, t… --- ## [\[Strategy Market\] Random Test](https://forum.eternagame.org/t/strategy-market-random-test/1828)
**Author:** [@paramodic](https://forum.eternagame.org/u/paramodic)\ **Replies:** 0\ **Last updated:** [July 9, 2013, 9:47pm UTC](https://forum.eternagame.org/t/strategy-market-random-test/1828 "2013-07-09T21:47:00Z")
I’m curious to see if random nucleotide placement will truly come out to .000. What I’m proposing for this strategy market is to randomly paint nucleotides until a solution is met or until the bot times out. [Previous page](https://forum.eternagame.org/c/strategy-market/25.md?page=1) [Next page](https://forum.eternagame.org/c/strategy-market/25.md?page=3)