Lab

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This article is an overview of the RNA lab process.

For the lab FAQ, click here (broken link)

Labs are type of puzzle in EteRNA where player solutions are synthesized and scored on their ability to fold properly. In each lab, players vote on their peers' designs to determine which are synthesized.

A player must earn 10,000 points to submit and vote on lab designs.

 

Contents

Introduction

Lab Steps Overview:

  1. Analysis - The lab archive is a treasure trove of data on what RNA designs folded successfully. Review successful designs to find winning strategies that get you more points!
  2. Design RNA - In lab puzzles, players are presented with a target structure which must be solved by making your own RNA designs.
  3. Scheduled Rounds - Each player may submit 3 lab designs and 3 votes per scheduled round.
  4. Submission & Voting - Once submitted, the player's designs are reviewed by other players, and votes are placed.
  5. Laboratory Synthesizing - The EteRNA team of scientists at Stanford's Das Lab then synthesizes the most popular design in a real laboratory.
  6. Design Scoring - Each design is awarded a score based on how well it folded to match its intended structure.
  7. Player Rewards - Points are rewarded according to the success demonstrated in the lab.

 

Lab Steps Explanation

Analysis

You will have the best chance at success if you learn from what has already been successful. Look at past labs, and find a similarly shaped RNA design that scored above 90 - open it up, and take a look at what bases were used where.

Can you see any winning patterns? Try them out! Of course, you can try new methods too, but if you're just starting out with labs and wondering how to get a good score, this is a great way to learn.

Types of Labs

  1. Classic Eterna - Early labs without barcodes
  2. FMN Aptamers - Early FMN aptamer labs
  3. Player Projects - Cloud lab beta
  4. Switches - Early switch labs
  5. Cloud Labs - All labs with barcodes - pretty much the whole archive except the last pages.

 

Design RNA

Once you have reviewed past lab data for successful designs, you are ready to design your very own RNA using solid strategies! You can also try new strategies, to gain insight into what does and does not work for a given type of RNA.

Previous labs have focused exclusively on satisfying a secondary structure, with many the target structures synthesized designed by players. Recently, EteRNA has moved to the design of aptamers and riboswitches.

Scheduled Rounds

Labs are organized and scheduled into rounds, with new rounds beginning every one to three weeks. A lab may continue for several rounds until a winner is found. Though synthesis and voting has stopped on old labs, players may continue to review old lab data and solve old lab puzzles.

 

Submission & Voting

A player may submit 3 sequences and vote on 8 sequences per round. Sequences that were not synthesized in previous rounds may be resubmitted. Players may vote on their own designs, but may only vote once on a given sequence.

 

Laboratory Synthesizing

The EteRNA team of scientists at Stanford's Das Lab then synthesizes the most popular design in a real laboratory. They perform science experiments in a real laboratory to determine our RNA designs' secondary structure and other chemical properties. This is where the real science happens!

This key step transforms our imagination from computer modelled RNA designs into real world research, so that we can analyze it and collect data. 

 

Design Scoring

Lab designs are analyzed after synthesis, and scored on a scale of 0-100 based on how well they satisfy the target structure. Scores of of 94 or higher are considered winning. A player's synthesized designs and their scores are visible on his or her player profile.

A synthesized design may be viewed via "Review Submitted Designs" and a representation of the SHAPE data may be viewed via "Color sequences based on experimental data" in addition to base colors as in the game.

A colorized graduated scale representing the SHAPE data for each base may be viewed by turning on the game option: "Use continuous colors for the exp. data".

These design results are important, since they help us understand what worked and what did not work, so that we can make even better designs on the next round. This is why reviewing successful designs from past labs ( step 1 ) before designing your RNA ( step 2 ) is a great strategy for improving your score!

 

Player Rewards

Players are awarded points for their submissions and votes, regardless of whether the sequences designed and voted on are synthesized.

For designs that are synthesized, the number of points awarded depends on synthesis score. For designs that are not synthesized, the reward is calculated based on the similarity of a sequence to those that have been synthesized.

Reward History: On Mar 22, 2013 a "News Item on new scoring method" in EteRNA news announced a new scoring system due to the large increase in synthesized solutions allowed by Cloud Lab.  The new  Design reward = lab_score*4, and Vote_reward = lab_score*2. Prior to that the rewards calculation was  Design reward = lab_score*20, and Vote_reward = lab_score*10.

 

Strategies

Main Article: Lab Strategies

Player-Created guides: Lab Guides

 

Boosting

The value of boosting in lab is unclear. Previous winners have included both boosted and unboosted designs. Certain special loop sequences with very low free energy appear strongly base paired, however.

 

GC/AU/GU Ratio

GC pairs are more stable than AU or GU pairs; however, designs with very high GC content are difficult to synthesize and likely to misfold. Designs contining exclusively GC pairs are unlikely to be voted for or synthesized. Likewise, designs that are very rich in AU or GU pairs are unlikely to be selected for synthesis.

 

Computational Tools

The EteRNA lab interface contains two computational tools that provide insight into the stability of the RNA being designed: the dot plot and the melt plot. Additionally, many secondary structure prediction programs are available on the web. The utility of these tools remains unclear.

 

Cooperation and Etiquette

Most experienced players are eager to help others design sequences. Design strategies are openly discussed in chat, on the forum, and in the wiki. The use of other players' designs as starting points is common. Newcomers to lab may find it especially helpful to modify an existing design rather than start from scratch.

Players are encouraged to acknowledge the original designer the sequence being modified. Asking for votes is considered impolite.

 

Overview of Lab Rounds

Here is a table for showing which batch a lab belongs to. It is useful knowing which round a lab belongs to because of the error rates of the lab data.  

Each synthesis round will have its own characteristics with respect to error rates. Each round is different. Sometimes, this is on purpose, as the lab tries to improve their process, and some times it is accidental, such as having reagents go bad for an unknown reason. Unlike the SHAPE values, the reported error rates are not normalized between rounds. So when comparing error rates between labs, it's important to know what rounds each of the labs were synthesized in. (Omei)

Each round number is connected to an rdat file and most rounds have spreadsheets with extracted data. The data is taken from RMDB (RNA Mapping Database). 

 

Round  Comments Labs  Signal-to-noise average

R0

12/21/2012

 

First batch of Player Projects

R0.xlsx

R0.googlesheet

Project : Thicker Zigzag
Project : Test of RNAfold (5)
Project : Test of RNAfold (4)
Project : Test of RNAfold (3)
Project : Test of RNAfold (2)
Project : Test of RNAfold (1)
Project : Multiloop: Two Pairs of Adjacent Stacks
Project : Testing various loop designs
Project : Hard Lab Fragments: Kudzu Arm
Project : Hard Lab Fragments: Kudzu Neck
Project : Hard Lab Fragments: Making it Up As I Go Multiloop
Project : Hard Lab Fragments: Water Strider Arm
Project : Neck Length 2 - 4 branch multiloop
Project : Bulge Sampler: 4-nt
Project : Bulge Sampler: 3-nt
Project : Bulge Sampler: 2-nt
Project : Bulge Sampler: 1-nt
Project : 3 single nucleotide bulges
Project : Isolated Base Pairs: 2-2 Loops Adjacent to Multiloop
Project : Isolated Base Pairs: Adjacent 2-1 Loops (1)
Project : Isolated Base Pairs: Adjacent 2-1 Loops (3)
Project : Isolated Base Pairs: Adjacent 2-1-Loops (4)
Project : Zigzag: 1-Nucleotide Bulge (4)
Project : Zigzag: 1-Nucleotide Bulge (3)
Project : Zigzag: 1-Nucleotide Bulge (2)
Project : Zigzag: 1-Nucleotide Bulge (1)
Project : GU-pin shape test
Project : comparison series: 2-10
Project : comparison series: 2-9
Project : comparison series: 2-8
Project : Crossroads test
Project : comparison series: 2-7
Project : comparison series: 2-6
Project : comparison series: 2-5
Project : comparison series: 2-4
Project : comparison series: 2-3
Project : Fisker - 2-2 loop energy challenge
Project : comparison series: 10-2
Project : comparison series: 9-2
Project : comparison series: 8-2
Project : comparison series: 7-2
Project : comparison series: 6-2
Project : comparison series: 5-2
Project : comparison series: 4-2
Project : Mat - comparison series: 3-2 - D1
Project : comparison series: Hairpin loop with 15 nts
Project : comparison series: Hairpin loop with 14 nts
Project : comparison series: Hairpin loop with 13 nts
Project : comparison series: Hairpin loop with 12 nts
Project : comparison series: Hairpin loop with 11 nts
Project : Mat - comparison series: Hairpin loop with 10 nts
Project : Mat - comparison series: Hairpin loop with 9 nts- D1
Project : Five Branch Multiloop
Project : comparison series: Octaloops
Project : comparison series: Heptaloop
Project : comparison series: Hexaloop 
Project : comparison series: Pentaloop 
Project : comparison series: Triloop 
Project : Multiloop: 4 Branches Separated by Single Unpaired Bases
Project : Multiloop: 3 Branches Unevenly Spaced (2)
Project : Multiloop: 3 Branches Unevenly Spaced (1)
Project : Multiloop: 3 Branches  12 Unpaired Bases
Project : Multiloop: 3 Branches  No Unpaired Bases
Project : 3-4 and 1-2 loops
Project : Chain length and loop size series 1-10
Project : chain lenth and loop size series 1-9
Project : chain length and loop size series 1-8
Project : chain length and loop size series 1-5
Project : chain length and loop size series 1-4
Project : chain lengh an loop size series 1-3
Project : comparison series: 1-15
Project : comparison series: 2-15
Project : comparison series: 3-15
Project : comparison series: 4-15
Project : comparison series: 5-15
Project : comparison series: 6-15
Project : comparison series: 7-15
Project : comparison series: 8-15
Project : comparison series: 9-15
Project : comparison series: 10-15
Project : comparison series: 11-15
Project : comparison series: 12-15
Project : comparison series: 13-15
Project : comparison series: 14-15
Project : comparison series: 15-1
Project : comparison series: 15-2
Project : comparison series: 15-3
Project : comparison series: 15-4
Project : comparison series: 15-5
Project : comparison series: 15-6
Project : comparison series: 15-7
Project : comparison series: 15-8
Project : comparison series: 15-9
Project : comparison series: 15-10
Project : comparison series: 15-11
Project : comparison series: 15-12
Project : comparison series: 15-13
Project : comparison series: 15-14
Project : comparison series: 15-15
Project : comparison series: 14-14
Project : comparison series: 13-13
Project : comparison series: 12-12
Project : comparison series: 11-11
Project : comparison series: 10-10
Project : comparison series: 9-9
Project : comparison series: 8-8
Project : comparison series: 7-7
Project : comparison series: 6-6
Project : comparison series:
Project : comparison series: 4-4
Project : comparison series:
Project : comparison series: 2-2
Project : comparison series: 1-1
Project : Two stacks
Project : Lab design for newer players
Project : Sample puzzle for lab
Project : Pseudoknot 2: Biotin-Binding Pseudoknot
Project : Pseudoknot 1: Minimal
Project : Half of The Branches
Project : Saccharomyces Cerevisiae Loop Structure
Project : 30 Nucleotide Loop 3 - Bulge Internal Loop
Project : Two bulges and a 1-2 loop (reverse)
Project : 30 Nucleotide Loop 2 - Asymmetric Internal Loop
Project : 30 Nucleotide Loop 1 - Symmetric Internal Loop
Project : Sharklike V-2 (SHAPE data Exp-2)
Project : Sharklike V-1 (SHAPE data Exp-1)
Project : S&E5 Modified
Project : Reshiram  Zekrom  Kyurem
Project : All red and blue
Project : Bulge test
Project : Guanine Reduction
Project : Uracil Reduction
Project : Large Isolated Hairpin
Project : Isolated Closing Pairs 3
Project : Alternative Mismatches
Project : Adenine Reduction
Project : Internal Loops: 5-2
Project : Internal Loops: 6-3
Project : FMN-RNA aptamer complex lab
Project : Tobramycin Aptamer
Project : Hairpins: Heptaloop
Project : Hairpins: Hexaloop
Project : Hairpins: Pentaloop
Project : Hairpins: Tetraloop
Project : Hairpins: Triloop
Project :  Chesterfield s-The Mousekateer
Project : Plain Hooked
Project : Nupack s Finger Revisited
Project : Large Loop
Project : Hooked
Project : Multiloop Isolated Closing Pairs
Project : Cytosine reduction
Project : Loop Heavy
Project : Fractal RNA
Project : Isolated Closing Pairs 2
Project : Repetitive Structures
Project : Isolated Closing Pairs 1
Project : 4-4 loop
Project : JerryP s winning design without tetraloop boost
Project : 2-2 loop
Project : Example project 2
Project : Example project
Shape Library 101: The Finger
Project: mRNA structure
Project: helix stacking
Project: all non-canonical pairs
Project : miRNA hairpin robustness
Project: metal ion pseudoknots
Project: VAI protein kinase R inhibitor
Project: unbound aptamer structures
Project: Parin s favorite motifs
therm1
 1.583

R1

4/9/2013

Second batch of Player Projects
Tested with four different SHAPE reagents:
Signal-to-Noise Averages not currently available  
 

R2

3/7/2013

Third batch of Player Projects
Tested with four different SHAPE reagents:
Each design was tested with each reagent twice, the second time with a different barcode
Signal-to-Noise Averages not currently available 

 
R69

R69.xlsx

R69.googlesheet

Cloud Lab 1 - Aires by wateronthemoon
Cloud Lab 2 - Triangle of doom version 2 by dstea
Cloud Lab 3 - A Simple Zigzag by janelle
Cloud Lab 4 - Random by theravin
Cloud Lab 5 - The Nonesuch by rnjensen45
Cloud Lab 6 - Cross by firedrake969
Cloud Lab 7 - 5 Fold Radial Asymmetrical Starfish Level 0 by Jieux
Cloud Lab 8 - Stellar Crossbow by jmf028
Cloud Lab 9 - Final Countdown by Tesla sDisciple
Cloud Lab 10 - Random Shape 2 by ElNando888
Cloud Lab 11 - Little bug by JR
Cloud Lab 12 - Anchor by ribonucleic
Cloud Lab 13 - Alien Party Glasses by Jennifer Pearl
Cloud Lab 14 - Easy loop sizes by Edward Lane
Cloud Lab 15 - Triloop Buffet by jandersonlee
Cloud Lab 16 - Section from lab Water Strider by Brourd
Cloud Lab 17 - Oryza sativa 8 Elements Part 2 by merryskies
Cloud Lab 18 - Anaconda About to Poop by SpaceFolder
Cloud Lab 19 - Big Hairpin Loop by Eli Fisker
Cloud Lab 20 - Random4 by mat747
 6.998
R70

Switch Cloud Labs  

LabPuz02 by JR
Bistable 3 by jnicol
Hair Trigger by space_miser
Will It Bind? by jmf028
Stratospheric by Dennis9600
Phase II - 1 by ElNando888
LS2 by c-quence
Anchor 2.0 by ribonucleic
Day 2 by wateronthemoon
Alive and kicking by Eli Fisker
Laydown and Jump by rnjensen45
McSwitch by Meechl
Water Snake Redux by jruaya
My Screw-Up Corrected? by SpaceFolder
Nincompoop by hoglahoo
Lines by starryjess
Bound state has a zigzag by stevetclark
Chirality by kcabral28
Switch Test 1 by Brourd
Top Notch by jmf028
 

R71

5/10/2013

R71.xlsx

R71.googlesheet

My Screw-Up Corrected? by SpaceFolder
Cloud Lab 1 - Aires by wateronthemoon
Cloud Lab 2 - Triangle of doom version 2 by dstea
Cloud Lab 3 - A Simple Zigzag by janelle
Cloud Lab 4 - Random by theravin
Cloud Lab 5 - The Nonesuch by rnjensen45
Cloud Lab 6 - Cross by firedrake969
Cloud Lab 7 - 5 Fold Radial Asymmetrical Starfish Level 0 by Jieux
Cloud Lab 8 - Stellar Crossbow by jmf028
Cloud Lab 9 - Final Countdown by Tesla sDisciple
Cloud Lab 10 - Random Shape 2 by ElNando888
Cloud Lab 11 - Little bug by JR
Cloud Lab 12 - Anchor by ribonucleic
Cloud Lab 13 - Alien Party Glasses by Jennifer Pearl
Cloud Lab 14 - Easy loop sizes by Edward Lane
Cloud Lab 15 - Triloop Buffet by jandersonlee
Cloud Lab 16 - Section from lab Water Strider by Brourd
Cloud Lab 17 - Oryza sativa 8 Elements Part 2 by merryskies
Cloud Lab 18 - Anaconda About to Poop by SpaceFolder
Cloud Lab 19 - Big Hairpin Loop by Eli Fisker
Cloud Lab 20 - Random4 by mat747
 3.698

R72

6/11/2013

R72.xlsx

R72.googlesheet

Ball & Chain by Krobar
Simplify by Tesla sDisciple
An Arm and a Leg 1.0 by kcabral28
Huffman by hotcreek
QRNAL0 by Quxwozing
Riboswitch-based by jruaya
1-X bulge testing   by Omei
EzFold by space_miser
Thursday by DHammond
TEBOWNED mutation - BH
TEBOWNED mutation - U
TEBOWNED mutation - B
Flu Virus
TEBOWNED reloaded
MedLoop
Ball & Chain by Krobar
Simplify by Tesla sDisciple
An Arm and a Leg 1.0 by kcabral28
Huffman by hotcreek
QRNAL0 by Quxwozing
Riboswitch-based by jruaya
1-X bulge testing by Omei
EzFold by space_miser
Thursday by DHammond
 4.272

R73

7/30/2013

R73.xlsx

R73.googlesheet

 

1-1-1-1-1-1 Multiloop
2-2 and 3-3 loops
A-U Closing Base Pairs
caulobacter_ncrna_lists
Hex-a-Stripe
Magic  boosts in 2-2 loops
Magic boosts in 2-2 loops revised  thanks starry
Permuted loops
Probing the 3D motif atlas
Quad Loop test
RNA Bridge
RNA Bridge (Updated)
RNA Strength
Short Stacks
Single state - Switch state
Single to Switch try  2
The GAAA loop
Tighter Two Stacks for 3-way Multi-Loop testing
Tribute To Satellite Kepler
Two stacks
Two Stacks - Triloop hairpin variation
Variations on a theme of 1-0 loops and short stack hairpins
 3.775

R73.0001

R73.0001.xlsx

R73.0001.googlesheet

 3.881
R74

R74.xlsx

R74.googlesheet

A-U Closing Base Pairs 2
Tetraloops and 0-0-0-0 Multiloop Phase 1
Tetraloops and 0-0-0-0 Multiloop Phase 1 Version 2
Lonely Base Pair - 1-1: Multiloop
Lonely Base Pair - 2-2: Multiloop
Lonely Base Pair - 3-3: Multiloop
FMN Switch 2.0 - First State with Locked Bases
Can We do it in 10? - FMN Switch 2.0
Triloop with multiloop core phase 1
Two Bulge Zigzag - Variation 1
Two Bulge Zigzag - Variation 3
Two Bulge Zigzag - Variation 4
G-U Closing Base Pairs
G-U Closing Base Pairs 2
Reversed G-C Multibranch Loop Closing Base Pairs
Probing for tertiary structure
Modeled Impossible: 31+ Nucleotide Internal Loops
RNA windows pilot project - 16s rRNA (3I1M)
Caulobacter ncRNA discovery
Tristable RNA
Hammerhead Ribozyme Wildtype Mutate and Map
MedLoop V2
Hammerhead Ribozyme G12A Mutate and Map
Entoplea bizarre tRNA 2D structure mt tRNA-Arg
 4.442
R75

R75.xlsx

R75.googlesheet

Short Stacks 2
SARS coronavirus structure test
FMN Binding Site Chemical Footprint
Modeled Impossible: 1 Nucleotide Bulge/Triloop Lonely base pair V1
New Frontier
Frog leg - Electric
ZigZag and ZagZig
Chicken leg
Chicken leg - Splayed
Motor Protein - Step 1
Motor Protein - Step 2
Motor Protein - Step 3
Intrinsically unfolded RNA
Probing the structure of  poly-A loops by mutation
PSTVd probing
Improving the Nearest Neighbor Energy Model Using EteRNA  Pilot
TCF21 3 UTR
MedLoop redux
 5.621

R76

8/23/2013

R76.xlsx

R76.googlesheet

Find Z - Here It Is!
Two Bulge  Zigzag  - Both Conformations
Two Bulge  Zigzag  - Variation 2
Modeled Impossible: 1 Nucleotide Bulge/Triloop Lonely base pair V2
TinkerToy Retread
Frog leg - relaxed
Frog leg - Stretched toe
Intersecting stacks 2
Is RNA directional 1 of 2
Semicircle - 2 bends
Semicircle - 5 bends
Location Dependent Chemical Footprints Part 1
Location Dependent Chemical Footprints Part 3
Location Dependent Chemical Footprints Part 4
Location Dependent Chemical Footprints Part 5
Location Dependent Chemical Footprints Part 6
Teeny tRNA
P5abc Mutants to Affect Folding Transitions
Testing 3D structure prediction of G/G mismatches (boosts!)
Testing for crazy conformations of tandem G/A and A/G pairs
A codon riboswitch
 3.692
R76.0001

R76.0001.xlsx

R76.0001.googlesheets

 3.389

R77

9/23/2013

R77.xlsx

R77.googlesheet

Intersecting stacks investigation
Is RNA directional 2 of 2
Semicircle - 3 bends
Semicircle -  4 bends
Location Dependent Chemical Footprints Part 2
Could Curves Survive?
Adding some sweet tetraloops
Palindromes part one
Dimer B
Dimer A
Robot serial killer 1 - Lab killer too?
Robot serial killer 2 - Lab killer too?
Short Stacks 3
Relaxed multiloop 2
New Frontier 2
Five Adjacent Stem Multibranch Loop
crRNA
tracrRNA
sgRNA89_NGS
sgRNA67
sgRNA48
Repeat hairpins v1
Codon riboswitch [repeat of tryptophan]
Codon riboswitch [arginine]
Class I ligase
MedLoop resurrected
Un-stable
M-stable
EteRNA R45-46 FMN Aptamer with Single Binding Site
EteRNA R43 the Backwards C
Codon riboswitch [histidine]
Reproducibility Lab 1
 1.714
R78

R78.xlsx

R78.googlesheet

Example project..
G-U GAGA Tetraloop Boost
Repetitious sequences
Robot serial killer 3 - Lab killer too?
FMN Shape Test- 1st State
FMN Shape Test- 2nd State
Wobble Quad Stability 1
SHAPE Profile - U-U Mismatch - Pilot Run
SHAPE Profile - C-U Mismatch - Pilot Run
SHAPE Profile - U-C Mismatch - Pilot Run
SHAPE Profile - C-A Mismatch - Pilot Run
SHAPE Profile - A-C Mismatch - Pilot Run
SHAPE Profile - G-A Mismatch - Pilot Run
SHAPE Profile - A-G Mismatch - Pilot Run
Unmodified tRNA sequences
Chicken Leg - Reversed
Reversed motor - step 1
Double 1-3 Loop
SHAPE Profile - C-C Mismatch - Pilot Run
Large GU stack
Neck strength analysis 3 of 3 - Weak - AUs + GUs.
Hexaloop Kd and SHAPE test
P5abc Mutants to Affect Folding Transitions 2
MedLoop Double Mutants - Shape 0
MedLoop delta Double Mutants - Shape 0
Bistable double mutants - Shape 0
M-stable double mutants - Shape 0
Un-stable double mutants - Shape 0
Bistable hairpin mutate and map - Shape 0
Un-stable alternative mutate-and-map - Shape 0
RPL11a Pseudouridylation Site Mutate and Map - Shape 0
TEF1 Pseudouridylation Site Mutate and Map - Shape 0
RPL11a Mutant Pseudouridylation Site Mutate and Map - Shape 0
Permuted Loops - Shape 0
Permuted Loops - Shape 1
Permuted Loops - Shape 2
Permuted Loops - Shape 3
Permuted Loops - Shape 4
Permuted Loops - Shape 5
Permuted Loops - Shape 6
Permuted Loops - Shape 7
Permuted Loops - Shape 8
Permuted Loops - Shape 9
Permuted Loops - Shape 10
Permuted Loops - Shape 11
Permuted Loops - Shape 12
Permuted Loops - Shape 13
Permuted Loops - Shape 14
Permuted Loops - Shape 15
Permuted Loops - Shape 16
Permuted Loops - Shape 17
Permuted Loops - Shape 18
Permuted Loops - Shape 19
Permuted Loops - Shape 20
Permuted Loops - Shape 21
Permuted Loops - Shape 22
Permuted Loops - Shape 23
Permuted Loops - Shape 24
Permuted Loops - Shape 25
Permuted Loops - Shape 26
Permuted Loops - Shape 27
Permuted Loops - Shape 28
Permuted Loops - Shape 29
Permuted Loops - Shape 30
Permuted Loops - Shape 31
Permuted Loops - Shape 32
Permuted Loops - Shape 33
Permuted Loops - Shape 34
Permuted Loops - Shape 35
Permuted Loops - Shape 36
Permuted Loops - Shape 37
Reproducibility Lab Another Round - Shape 0
Reproducibility Lab Another Round - Shape 1
Reproducibility Lab Another Round - Shape 2
Reproducibility Lab Another Round - Shape 3
Reproducibility Lab Another Round - Shape 4
Reproducibility Lab Another Round - Shape 5
Reproducibility Lab Another Round - Shape 6
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Reproducibility Lab Another Round - Shape 16
Reproducibility Lab Another Round - Shape 17
Reproducibility Lab Another Round - Shape 18
Reproducibility Lab Another Round - Shape 19
Reproducibility Lab Another Round - Shape 20
Influenza PB2 mutant sequences - Shape 0
Influenza PB2 mutant sequences - Shape 1
Single strand barcodes - Shape 0
Single strand barcodes - Shape 1
Single strand barcodes - Shape 2
Single strand barcodes - Shape 3
 2.604
R79

R79.xlsx

R79.googlesheet

Test of locking loop bases in a ribozyme-like structure
Relaxed multiloop 1
Relaxed multiloop 3
Reversed motor - Step 2
Reversed motor - Step 3
Reversed motor - Step 4
A-U Closing Base Pairs 3
A-U Closing Base Pairs 4
T.thermophilise16S Hammerhead
Alien partial glasses - Mirror version
Single to Switch try  2 - Mirror version
Let s break the barcode
Don Quixote
Mummiebrain s M2
Impossible Folding II - The Intramolecular G-quadruplex
PB2elem2_MR_syn - Shape 0
GNRA/receptor project - Shape 0
GNRA/receptor project - Shape 1
GNRA/receptor project - Shape 2
GNRA/receptor project - Shape 3
CR4-5 domain of human telomerase - Shape 0
CR4-5 domain of human telomerase - Shape 1
CR4-5 domain of human telomerase - Shape 2
CR4-5 domain of human telomerase - Shape 3
CR4-5 domain of human telomerase - Shape 4
CR4-5 domain of human telomerase - Shape 5
CR4-5 domain of human telomerase - Shape 6
CR4-5 domain of human telomerase - Shape 7
CR4-5 domain of human telomerase - Shape 8
CR4-5 domain of human telomerase - Shape 9
CR4-5 domain of human telomerase - Shape 10
CR4-5 domain of human telomerase - Shape 11
CR4-5 domain of human telomerase - Shape 12
CR4-5 domain of human telomerase - Shape 13
CR4-5 domain of human telomerase - Shape 14
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CR4-5 domain of human telomerase - Shape 39
CR4-5 domain of human telomerase - Shape 40
CR4-5 domain of human telomerase - Shape 41
CR4-5 domain of human telomerase - Shape 42
CR4-5 domain of human telomerase - Shape 43
CR4-5 domain of human telomerase - Shape 44
CR4-5 domain of human telomerase - Shape 45
CR4-5 domain of human telomerase - Shape 46
CR4-5 domain of human telomerase - Shape 47
CR4-5 domain of human telomerase - Shape 48
CR4-5 domain of human telomerase - Shape 49
CR4-5 domain of human telomerase - Shape 50
CR4-5 domain of human telomerase - Shape 51
CR4-5 domain of human telomerase - Shape 52
CR4-5 domain of human telomerase - Shape 53
CR4-5 domain of human telomerase - Shape 54
CR4-5 domain of human telomerase - Shape 55
CR4-5 domain of human telomerase - Shape 56
CR4-5 domain of human telomerase - Shape 57
RF01020 mutate-and-map - Shape 0
RF01020 mutate-and-map - Shape 1
RF01020 mutate-and-map - Shape 2
RF01020 mutate-and-map - Shape 3
RF01020 mutate-and-map - Shape 4
RF01020 mutate-and-map - Shape 5
RF01020 mutate-and-map - Shape 6
RF01020 mutate-and-map - Shape 7
RF01020 mutate-and-map - Shape 8
RF01020 mutate-and-map - Shape 9
RF01020 mutate-and-map - Shape 10
RF01020 mutate-and-map - Shape 11
RF01020 mutate-and-map - Shape 12
RF01020 mutate-and-map - Shape 13
RF01020 mutate-and-map - Shape 14
RF01020 mutate-and-map - Shape 15
RF01020 mutate-and-map - Shape 16
RF01020 mutate-and-map - Shape 17
RF01020 mutate-and-map - Shape 18
RF01020 mutate-and-map - Shape 19
RF01020 mutate-and-map - Shape 20
RF01020 mutate-and-map - Shape 21
RF01020 mutate-and-map - Shape 22
RF01020 mutate-and-map - Shape 23
RF01020 mutate-and-map - Shape 24
RF01020 mutate-and-map - Shape 25
RF01020 mutate-and-map - Shape 26
RF01020 mutate-and-map - Shape 27
RF01020 mutate-and-map - Shape 28
RF01020 mutate-and-map - Shape 29
RF01020 mutate-and-map - Shape 30
RF01020 mutate-and-map - Shape 31
RF01020 mutate-and-map - Shape 32
RF01020 mutate-and-map - Shape 33
RF01020 mutate-and-map - Shape 34
RF01020 mutate-and-map - Shape 35
RF01020 mutate-and-map - Shape 36
RF01020 mutate-and-map - Shape 37
RF01414 mutate-and-map - Shape 0
RF01414 mutate-and-map - Shape 1
RF01414 mutate-and-map - Shape 2
RF01414 mutate-and-map - Shape 3
RF01414 mutate-and-map - Shape 4
RF01414 mutate-and-map - Shape 5
RF01414 mutate-and-map - Shape 6
RF01414 mutate-and-map - Shape 7
RF01414 mutate-and-map - Shape 8
RF01414 mutate-and-map - Shape 9
RF01414 mutate-and-map - Shape 10
RF01414 mutate-and-map - Shape 11
RF01414 mutate-and-map - Shape 12
RF01414 mutate-and-map - Shape 13
RF01414 mutate-and-map - Shape 14
RF01414 mutate-and-map - Shape 15
RF01414 mutate-and-map - Shape 16
RF01414 mutate-and-map - Shape 17
RF01414 mutate-and-map - Shape 18
RF01414 mutate-and-map - Shape 19
RF01414 mutate-and-map - Shape 20
RF01414 mutate-and-map - Shape 21
RF01414 mutate-and-map - Shape 22
RF01414 mutate-and-map - Shape 23
RF01414 mutate-and-map - Shape 24
RF01414 mutate-and-map - Shape 25
RF01414 mutate-and-map - Shape 26
RF01414 mutate-and-map - Shape 27
RF01125 mutate-and-map - Shape 0
RF01125 mutate-and-map - Shape 1
RF01125 mutate-and-map - Shape 2
RF01125 mutate-and-map - Shape 3
RF01125 mutate-and-map - Shape 4
RF01125 mutate-and-map - Shape 5
RF01125 mutate-and-map - Shape 6
RF01125 mutate-and-map - Shape 7
RF01125 mutate-and-map - Shape 8
RF01125 mutate-and-map - Shape 9
RF01125 mutate-and-map - Shape 10
RF01125 mutate-and-map - Shape 11
RF01125 mutate-and-map - Shape 12
RF01125 mutate-and-map - Shape 13
RF01125 mutate-and-map - Shape 14
RF01125 mutate-and-map - Shape 15
RF01125 mutate-and-map - Shape 16
RF01125 mutate-and-map - Shape 17
RF01125 mutate-and-map - Shape 18
RF01125 mutate-and-map - Shape 19
RF01125 mutate-and-map - Shape 20
RF01125 mutate-and-map - Shape 21
RF01125 mutate-and-map - Shape 22
RF01125 mutate-and-map - Shape 23
RF01125 mutate-and-map - Shape 24
RF01125 mutate-and-map - Shape 25
RF01125 mutate-and-map - Shape 26
RF01125 mutate-and-map - Shape 27
RF01125 mutate-and-map - Shape 28
RF01125 mutate-and-map - Shape 29
RF01125 mutate-and-map - Shape 30
 3.046

R80

2/5/2014

R80.xlsx

R80.googlesheet

Wobble Quad Control 2
Wobble Quad Control 3
Wobble Quad Control 4
SHAPE Profile - G-G Mismatch - Pilot Run
Reversed G-C Multibranch Loop Closing Base Pairs 2
SHAPE Profile - U-U Mismatch - Pilot Run 2A
SHAPE Profile - U-U Mismatch - Pilot Run 2B
SHAPE Profile - A-G Mismatch - Pilot Run 2A
SHAPE Profile - A-G Mismatch - Pilot Run 2B
Tetraloop Competition Series - GAAA
Tetraloop Competition - UUCG
Tetraloop Competition Series - UACG
Tetraloop Competition Series - GAGA
SHAPE Profile - A-A Mismatch - Pilot Run
Repeatability - Melted Helix Variation 1
Repeatability - Melted Helix Variation 2
SHAPE Profile - Most Likely Base Pair C/G
Really big loop coil - Classic science toy
Intrinsical - Frequency 1
Intrinsical - Frequency 8
Impossible Folding I
Poly (A) Structure Analysis 1
New Frontier 3
Cobalamin Riboswitches  - Shape 0
Cobalamin Riboswitches  - Shape 1
Cobalamin Riboswitches  - Shape 2
Cobalamin Riboswitches  - Shape 3
Cobalamin Riboswitches  - Shape 5
Cobalamin Riboswitches  - Shape 11
Cobalamin Riboswitches  - Shape 12
Cobalamin Riboswitches  - Shape 14
Cobalamin Riboswitches  - Shape 19
Cobalamin Riboswitches  - Shape 23
Motif Assembled GAAA tetraloop binders - Shape 0
The RFAM Mapping project - Shape 0
The RFAM Mapping project - Shape 1
The RFAM Mapping project - Shape 2
The RFAM Mapping project - Shape 3
The RFAM Mapping project - Shape 4
The RFAM Mapping project - Shape 5
The RFAM Mapping project - Shape 6
The RFAM Mapping project - Shape 7
The RFAM Mapping project - Shape 8
The RFAM Mapping project - Shape 9
The RFAM Mapping project - Shape 10
The RFAM Mapping project - Shape 11
The RFAM Mapping project - Shape 12
The RFAM Mapping project - Shape 13
The RFAM Mapping project - Shape 14
The RFAM Mapping project - Shape 15
The RFAM Mapping project - Shape 16
The RFAM Mapping project - Shape 17
The RFAM Mapping project - Shape 18
The RFAM Mapping project - Shape 19
The RFAM Mapping project - Shape 20
The RFAM Mapping project - Shape 21
The RFAM Mapping project - Shape 22
The RFAM Mapping project - Shape 23
The RFAM Mapping project - Shape 24
The RFAM Mapping project - Shape 25
The RFAM Mapping project - Shape 26
The RFAM Mapping project - Shape 27
The RFAM Mapping project - Shape 28
The RFAM Mapping project - Shape 29
The RFAM Mapping project - Shape 30
The RFAM Mapping project - Shape 31
The RFAM Mapping project - Shape 32
The RFAM Mapping project - Shape 33
The RFAM Mapping project - Shape 34
The RFAM Mapping project - Shape 35
The RFAM Mapping project - Shape 36
The RFAM Mapping project - Shape 37
The RFAM Mapping project - Shape 38
The RFAM Mapping project - Shape 39
The RFAM Mapping project - Shape 40
The RFAM Mapping project - Shape 41
The RFAM Mapping project - Shape 42
The RFAM Mapping project - Shape 43
The RFAM Mapping project - Shape 44
The RFAM Mapping project - Shape 45
The RFAM Mapping project - Shape 46
The RFAM Mapping project - Shape 47
The RFAM Mapping project - Shape 48
The RFAM Mapping project - Shape 49
The RFAM Mapping project - Shape 50
The RFAM Mapping project - Shape 51
The RFAM Mapping project - Shape 52
The RFAM Mapping project - Shape 53
The RFAM Mapping project - Shape 54
The RFAM Mapping project - Shape 55
The RFAM Mapping project - Shape 56
The RFAM Mapping project - Shape 57
The RFAM Mapping project - Shape 58
The RFAM Mapping project - Shape 59
The RFAM Mapping project - Shape 60
The RFAM Mapping project - Shape 61
The RFAM Mapping project - Shape 62
The RFAM Mapping project - Shape 63
The RFAM Mapping project - Shape 64
The RFAM Mapping project - Shape 65
The RFAM Mapping project - Shape 66
The RFAM Mapping project - Shape 67
The RFAM Mapping project - Shape 68
The RFAM Mapping project - Shape 69
The RFAM Mapping project - Shape 70
The RFAM Mapping project - Shape 71
The RFAM Mapping project - Shape 72
The RFAM Mapping project - Shape 73
The RFAM Mapping project - Shape 74
The RFAM Mapping project - Shape 75
The RFAM Mapping project - Shape 76
The RFAM Mapping project - Shape 77
The RFAM Mapping project - Shape 78
The RFAM Mapping project - Shape 79
The RFAM Mapping project - Shape 80
The RFAM Mapping project - Shape 81
The RFAM Mapping project - Shape 82
The RFAM Mapping project - Shape 83
The RFAM Mapping project - Shape 84
The RFAM Mapping project - Shape 85
The RFAM Mapping project - Shape 86
The RFAM Mapping project - Shape 87
The RFAM Mapping project - Shape 88
The RFAM Mapping project - Shape 89
The RFAM Mapping project - Shape 90
The RFAM Mapping project - Shape 91
The RFAM Mapping project - Shape 92
The RFAM Mapping project - Shape 93
The RFAM Mapping project - Shape 94
The RFAM Mapping project - Shape 95
The RFAM Mapping project - Shape 96
The RFAM Mapping project - Shape 97
The RFAM Mapping project - Shape 98
Nando s Zippers - Shape 0
Ambiguous Bulges - Shape 0
Ambiguous Bulges - Shape 1
Ambiguous Bulges - Shape 2
Ambiguous Bulges - Shape 3
 2.217

R81

2/4/2014

R81.xlsx

R81.googlesheets

Dimer A - control
Small Loops- v. 1
SHAPE Profile - G-G Mismatch - Pilot Run 2A
SHAPE Profile - G-G Mismatch - Pilot Run 2B
SHAPE Profile - A-A Mismatch - Pilot Run 2B
Simplify - Mirror version
SHAPE Profile - Most Likely Base Pair G/C
Early bulge
Really big loop coil - control
Intrinsical frequency
Intrinsically Green
Intrinsically Blue
Very relaxed multiloop
Intrinsical - Frequency 2
Intrinsical - Frequency 6
Intrinsical - Frequency 7
TrpBoundState
TrpAltA
TrpAltB
TrpAltC
GNRA/receptor project - Shape 0
GNRA/receptor project - Shape 1
GNRA/receptor project - Shape 2
GNRA/receptor project - Shape 3
GNRA/receptor project - Shape 4
GNRA/receptor project - Shape 5
GNRA/receptor project - Shape 8
GNRA/receptor project - Shape 12
 2.620

R82

2/5/2014

R82.xlsx

R82.googlesheet

Improving the Energy Model: Competing Tetraloops  Part 1
Ziggy 25 (aka Multiloop Test)
Reversed G-C Multibranch Loop Closing Base Pairs 3
SHAPE Profile - A-C Mismatch - Pilot Run 2A
SHAPE Profile - G-A Mismatch - Pilot Run 2B
Neck strength analysis 1 of 3 - Strong - alternating GCs.
Neck strength analysis 2 of 3 - Medium - alternating AUs.
SHAPE Profile - C-C Mismatch - Pilot Run 2B
SHAPE Profile - A-A Mismatch - Pilot Run 2A
Late bulge
Late bulge control
Intrinsically Red
Intrinsical - Frequency 3
Intrinsical - Frequency 4
Short Neck and Split Ends
Adding some sweet triloops
Ribozyme 1: Hammerhead variant
JR s Let s Break the Barcode - 2 nt Dangling End Gap
JR s Let s Break the Barcode - 3 nt Dangling End Gap
Improving the Energy Model: Favoring an Equivalent Structure
Improving the Energy Model: 5-Base Hairpin Loops
Reproducibility Lab Round 3 - Shape 0
Reproducibility Lab Round 3 - Shape 1
Reproducibility Lab Round 3 - Shape 2
Reproducibility Lab Round 3 - Shape 3
Reproducibility Lab Round 3 - Shape 4
Reproducibility Lab Round 3 - Shape 5
Reproducibility Lab Round 3 - Shape 6
Reproducibility Lab Round 3 - Shape 7
Reproducibility Lab Round 3 - Shape 8
Reproducibility Lab Round 3 - Shape 9
Reproducibility Lab Round 3 - Shape 10
Reproducibility Lab Round 3 - Shape 11
Reproducibility Lab Round 3 - Shape 12
Reproducibility Lab Round 3 - Shape 13
Reproducibility Lab Round 3 - Shape 14
Reproducibility Lab Round 3 - Shape 15
Reproducibility Lab Round 3 - Shape 16
Reproducibility Lab Round 3 - Shape 17
Reproducibility Lab Round 3 - Shape 18
Reproducibility Lab Round 3 - Shape 19
Reproducibility Lab Round 3 - Shape 20
Motif Assembled GAAA tetraloop binders - Shape 0
Motif Assembled GAAA tetraloop binders - Shape 1
Motif Assembled GAAA tetraloop binders - Shape 2
Motif Assembled GAAA tetraloop binders - Shape 4
Motif Assembled GAAA tetraloop binders - Shape 6
Motif Assembled GAAA tetraloop binders - Shape 7
Motif Assembled GAAA tetraloop binders - Shape 8
Motif Assembled GAAA tetraloop binders - Shape 10
Motif Assembled GAAA tetraloop binders - Shape 11
Johan s sequences
 2.989

R83

3/27/2014

P4-P6 domain  Tetrahymena ribozyme was also run,
but only in R83, not R83.2 or R83.3
R83.xlsx
Wobble Quad Stability 2
Wobble Quad Stability 3
Wobble Quad Stability 4
Wobble Quad Control 1
SHAPE Profile - C-U Mismatch - Pilot Run 2A
SHAPE Profile - C-A Mismatch - Pilot Run 2B
SHAPE Profile - A-C Mismatch - Pilot Run 2B
SHAPE Profile - G-A Mismatch - Pilot Run 2A
SHAPE Profile - C-C Mismatch - Pilot Run 2A
Early bulge control
Intrinsical - Frequency 5
Triloop Hairpin and Stem Loop - Helix Stability
The G Quadruplex - Round 2
New Frontier 4
SAM II Riboswitch
1.946 

R83.0002

4/1/2014

 

R83.0002.xlsx

R83.0002.googlesheet

 4.907

R83.0003

4/3/2014

 

R83.0003.xlsx

R83.0003.googlesheet

 5.690

R84

4/21/2014

R84.xlsx

R84.googlesheet

FMN Binding Site - Rotated
SHAPE Profile - C-U Mismatch - Pilot Run 2B
SHAPE Profile - Most Likely Base Pair U/A - Variation 1.1
Most Likely Base Pair U/A - Variation 1.1B
SHAPE Profile - Most Likely Base Pair U/A - Variation 1.3
SHAPE Profile - Most Likely Base Pair G/C - Variation 2
SHAPE Profile - Most Likely Base Pair G/C - Variation 2B
Kinky Bits
JR s Let s Break the Barcode - Adjacent Barcode Version
The Donkey s Tail
A-U Closing Base Pairs - 4.1
A-U Closing Base Pairs - 4.2
G-U Closing Base Pairs - 4.3
G-U Closing Base Pairs - 4.4
Motif study: the S-turn
Consensus
Pure A
GA mismatch only
G14A
Alternative  C-C mismatch
Alternative  U-C mismatch
Alternative  U-C & A-C mismatches
G12A
Mad multiloop - Pentaloop 1
Pentaloop 2
Pentaloop 3
Hexaloop 1
Hexaloop 2
Hexaloop 3
Neck-Hairpin Spacing 3
Neck-Hairpin Spacing 1
Neck-Hairpin Spacing 0
Neck-Hairpin Spacing 2
Return of the boost
Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 6
Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 5
Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 4
Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 3
Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 2
Multibranch Loop Terminal Mismatch Stability Pilot - Strand Length 1
Hairpin ribozyme
Variant 1
Variant 2
RNA Transient Structures and pre-miRs - Shape 0
RNA Transient Structures and pre-miRs - Shape 1
RNA Transient Structures and pre-miRs - Shape 2
RNA Transient Structures and pre-miRs - Shape 3
RNA Transient Structures and pre-miRs - Shape 4
RNA Transient Structures and pre-miRs - Shape 5
RNA Transient Structures and pre-miRs - Shape 6
RNA Transient Structures and pre-miRs - Shape 7
RNA Transient Structures and pre-miRs - Shape 10
 2.725

R85

5/9/2014

R85.xlsx

R85.googlesheet

SHAPE Profile - Most Likely Base Pair U/A - Variation 1.2
SHAPE Profile - Most Likely Base Pair U/A - Variation 1.4
SHAPE Profile - Most Likely Base Pair C/G - Variation 2
SHAPE Profile - Most Likely Base Pair C/G - Variation 2B
GGG/UCC Wobble Closing Base Pairs - Hexaloop RE
GGG/UCC Wobble Closing Base Pairs - Heptaloop
5  Hairpin Stem  Part 1 - Five Base Pairs + UUCG Tetraloop
Stabilise the 1-1-1-1-1 multiloop
FMN in zigzag
L3-9
L3-8
L3-7
L3-6
L3-5
L3-4
Helix Comparison - 4x4 Loop
Helix Comparison - 5x5 Loop
Helix Comparison - 6x6 Loop
Helix Comparison - Four Base Pair Stem
Helix Comparison - Eight Base Pair Stem
Helix Comparison - Stem 2 G-U
Helix Comparison - Stem 1 G-U
New Frontier 5
Telephone
Effect of Bulge Proximity on RNA Stability
Effect of Bulge Proximity on RNA Stability:  More Distance
FMN Mimic Pilot - (CCUAUC/GAAGG & AGUAUA/UAACA) 1
FMN Mimic Pilot - (CCUAUC/GAAGG & AGUAUA/UAACA) 2
FMN Mimic Pilot - AGUAUA/UAACA
FMN Mimic Pilot - (GUAGUA/GAAAC & AGGAUA/UAAUU)
FMN Mimic Pilot - (UGUAUU/GAAGG & UGGAUA/GACGG)
FMN Mimic Pilot - (CUGAAC/GACGG & CGUUAC/GGAGG)
FMN Mimic Pilot - (AGGAUA/UACUG & AGGAUA/UAAGG)
FMN Mimic Pilot - (CUGAGC/GACGG & CGGAUA/GACGG)
Unbound
Bound - Mimic CCUAUC--GAAGG
Bound - Mimic GUAGUA--GAAAC
Bound - Mimic UGUAUU--GAAGG
Bound - Mimic AGGAUA--UAAUU
Bound - Mimic UGGAUA--GACGG
Bound - Mimic CUGAAC--GACGG
Bound - Mimic AGUAUA--UAACA
Bound - Mimic CGUUAC--GGAGG
Aptamer secondary structure - Shape 2
Aptamer secondary structure - Shape 5
Aptamer secondary structure - Shape 6
Aptamer secondary structure - Shape 7
Aptamer secondary structure - Shape 8
Reproducibility Lab 2 - Shape 0
Reproducibility Lab 2 - Shape 1
Reproducibility Lab 2 - Shape 2
Reproducibility Lab 2 - Shape 3
Reproducibility Lab 2 - Shape 4
Reproducibility Lab 2 - Shape 5
Reproducibility Lab 2 - Shape 6
Reproducibility Lab 2 - Shape 7
Reproducibility Lab 2 - Shape 8
Reproducibility Lab 2 - Shape 9
Reproducibility Lab 2 - Shape 10
Reproducibility Lab 2 - Shape 11
Reproducibility Lab 2 - Shape 12
Reproducibility Lab 2 - Shape 13
Reproducibility Lab 2 - Shape 14
Reproducibility Lab 2 - Shape 15
Reproducibility Lab 2 - Shape 16
Reproducibility Lab 2 - Shape 17
Reproducibility Lab 2 - Shape 18
Reproducibility Lab 2 - Shape 19
Reproducibility Lab 2 - Shape 20
Stanford Switch Puzzle
 2.295

R86

6/9/2014

R86.xlsx

R86.googlesheet

20% Non Watson-Crick Base Pairs - Effortless
40% Non Watson-Crick Base Pairs - Medium
60% Non Watson-Crick Base Pairs - Heating Up
70% Non Watson-Crick Base Pairs - Hard Mode
80% Non Watson-Crick Base Pairs - Insanity
Hand and Finger Remade - OFF State
Hand and Finger Remade - Mimic
Simple RNA Switch Remade - OFF State
Simple RNA Switch Remade - Mimic
Hair Trigger - Sub 2 (Stable) by Brourd: -2.51 Kcal/mol Mimic Bonus
Hair Trigger - Sub 2 (Stable) by Brourd: -4.86 Kcal/mol Mimic Bonus
Bistable 3 - Mod of Eli by mat747: -2.51 Kcal/mol Mimic Bonus
Bistable 3 - Mod of Eli by mat747: -4.86 Kcal/mol Mimic Bonus
Identify tRNA Mutants Subject to Alternative RNA Processing - Shape 0
Investigation of Alternative Human tRNA Structures - Shape 4
Investigation of Alternative Human tRNA Structures - Shape 5
Investigation of Alternative Human tRNA Structures - Shape 14
Investigation of Alternative Human tRNA Structures - Shape 15
Investigation of Alternative Human tRNA Structures - Shape 16
Investigation of Alternative Human tRNA Structures - Shape 17
Investigation of Alternative Human tRNA Structures - Shape 18
Investigation of Alternative Human tRNA Structures - Shape 19
Investigation of Alternative Human tRNA Structures - Shape 23
Investigation of Alternative Human tRNA Structures - Shape 25
Investigation of Alternative Human tRNA Structures - Shape 28
Investigation of Alternative Human tRNA Structures - Shape 36
Alternative structure space for human tRNAs - Shape 4
Alternative structure space for human tRNAs - Shape 5
Alternative structure space for human tRNAs - Shape 14
Alternative structure space for human tRNAs - Shape 15
Alternative structure space for human tRNAs - Shape 16
Alternative structure space for human tRNAs - Shape 17
Alternative structure space for human tRNAs - Shape 18
Alternative structure space for human tRNAs - Shape 19
Alternative structure space for human tRNAs - Shape 23
Alternative structure space for human tRNAs - Shape 25
Alternative structure space for human tRNAs - Shape 28
Alternative structure space for human tRNAs - Shape 36
 3.217

R87

8/18/2014

R87.xlsx

R87.googlesheet

 

Lab Entry Level 0 - The Finger lab revisited - Frozen shape with gap size 0
Lab Entry Level 0 - The Finger lab revisited - Frozen shape with gap size 4
Lab Entry Level 1 - The Finger lab revisited - Gap size 2
Lab Entry Level 2 - The Finger lab modified - Gap size 2
Poly (A) Structure Analysis 2
Multistate RNA Sequence - 2 Residues
Multistate RNA Sequence - 3 Residues
Multistate RNA Sequence - 4 Residues
Hairpin Loop Comparison Pilot - Shape 0
Hairpin Loop Comparison Pilot - Shape 1
Hairpin Loop Comparison Pilot - Shape 2
Hairpin Loop Comparison Pilot - Shape 3
Hairpin Loop Comparison Pilot - Shape 4
Hairpin Loop Comparison Pilot - Shape 5
Hairpin Loop Comparison Pilot - Shape 6
Hairpin Loop Comparison Pilot - Stem Comparison Tests
SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs GNCgaaaaGNC - Shape 0
SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs GNCgaaaaGNC - Shape 1
SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs CNGgaaaaCNG - Shape 0
SHAPE Profile - G/A Hairpin Terminal Mismatch and Neighboring Base Pairs CNGgaaaaCNG - Shape 1
Multistate RNA - CC/G bulge - Shape 0
Cyanocobalamin (vitamin B12) RNA aptamer SHAPE profile - Shape 0
Sarcin-ricin vs boosted internal loops - Shape 0
Sarcin-ricin vs boosted internal loops - Shape 1
Sarcin-ricin vs boosted internal loops - Shape 2
Sarcin-ricin vs boosted internal loops - Shape 3
Sarcin-ricin vs boosted internal loops - Shape 4
Sarcin-ricin vs boosted internal loops - Shape 5
Sarcin-ricin vs boosted internal loops - Shape 6
2-2 Superboost
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 0
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 1
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 2
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 3
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 4
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 5
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 6
Apical Loop Comparison - Dissimilar Stem Sequences - Shape 7
Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 0
Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 1
Effects of Base Pair Mutations on the RNA Ensemble and Reverse Transcription - Shape 2
Identify tRNA Mutants Subject to Alternative RNA Processing - Shape 0
Alternative structure space for human tRNAs - Shape 4
Alternative structure space for human tRNAs - Shape 5
Alternative structure space for human tRNAs - Shape 14
Alternative structure space for human tRNAs - Shape 15
Alternative structure space for human tRNAs - Shape 16
Alternative structure space for human tRNAs - Shape 17
Alternative structure space for human tRNAs - Shape 18
Alternative structure space for human tRNAs - Shape 19
Alternative structure space for human tRNAs - Shape 23
Alternative structure space for human tRNAs - Shape 25
Alternative structure space for human tRNAs - Shape 28
Alternative structure space for human tRNAs - Shape 36
 1.004

R87.0001

8/21/2014

R87.xlsx

R87.googlesheet

 1.731

R87.0002

8/21/2014

R87.xlsx

R87.googlesheet

1.109

R88

8/27/2014

R88.xlsx

R88.googlesheet

Lab Entry Level 0 - The Cross lab revisited - Frozen shape with gap size 0
Lab Entry Level 0 - The Cross lab revisited - Frozen shape with gap size 4
Lab Entry Level 1 - The Cross lab revisited - Gap size 2
Lab Entry Level 2 - The Cross lab modified - Gap size 2
 0.918
R88.0002   5.627

R89

R89.xlsx

R89.googlesheet

Switch Cloud Lab: The Next Generation 4 - OFF
Switch Cloud Lab: The Next Generation 4 - MIMIC
Hair Trigger - Sub 2 (Stable) by Brourd: -2.51 Kcal/mol Mimic Bonus R2
Bistable 3 - Mod of Eli by mat747: -2.51 Kcal/mol Mimic Bonus R2
Bistable 3 - Double Trouble by Darkfire47: -2.51 Kcal/mol Mimic Bonus
Hair Trigger - Reresub 3 (Unstable) by Brourd: -2.51 Kcal/mol Mimic Bonus
Pseudo-Titration Experiment: Lines - Errazaarge by ViennaUCT
Lab Entry Level 0 - Bulge Cross revisited - Frozen shape with gap size 0
Lab Entry Level 0 - Bulge Cross revisited - Frozen shape with gap size 4
Lab Entry Level 1 - Bulge Cross lab revisited - Gap size 2
Lab Entry Level 2 - Bulge Cross lab modified - Gap size 2
3.149
R90

R90.xlsx

R90.googlesheet

Lab Entry Level 0 - Bend and Ends Sampler revisited - Frozen shape with gap size 0
Lab Entry Level 0 - Bend and Ends Sampler revisited - Frozen shape with gap size 4
Lab Entry Level 1 - Bend and Ends Sampler revisited - Frozen shape with gap size 2
Lab Entry Level 2 - Bends and Ends Sampler modified - Gap size 2
1.037
R91

R91.xlsx

R90.googlesheet

Lab Entry Level 0 - The Asymmetry lab revisited - Frozen shape with gap size 0
Lab Entry Level 0 - The Asymmetry lab revisited - Frozen shape with gap size 4
Lab Entry Level 1 - The Asymmetry lab revisited - Gap size 2
Lab Entry Level 2 - The Asymmetry lab modified - Gap size 2
S1-KL1
S1-KL1-noGU
S1-KL-negative
S1-KL-1S72_423
S1-KL-new_A
S1-KL-new_B
S2-KL1
S2-KL1-noGU
S2-KL-negative
S2-KL-1S72_423
S2-KL-new_A
S2-KL-new_B
4/4 Base Pairs 5
5/5 Base Pairs 5
6/6 Base Pairs 5
7/7 Base Pairs 5
4/4 Base Pairs 3
5/5 Base Pairs 3
6/6 Base Pairs 3
7/7 Base Pairs 3
Shift 4/4 Base Pairs 5
Shift 5/4 Base Pairs 5
Shift 6/4 Base Pairs 5
Shift 5/5 Base Pairs 3
Shift 6/5 Base Pairs 3
Shift 7/5 Base Pairs 3
2.364
R92

R92.xlsx

R92.googlesheet

Lab Entry Level 0 - The Backwards C lab revisited - Frozen shape with gap size 0
Lab Entry Level 0 - The Backwards C lab revisited - Frozen shape with gap size 4
Lab Entry Level 1 - The Backwards C lab revisited - Gap size 2
Lab Entry Level 2 - The Backwards C lab modified - Gap size 2
4 x 4 TEP Riboswitch 5
5 x 5 TEP Riboswitch 5
6 x 6 TEP Riboswitch 5
4 x 4 TEP Riboswitch 3
5 x 5 TEP Riboswitch 3
6 x 6 TEP Riboswitch 3
Shift 5 x 5 TEP Riboswitch 5
Shift 6 x 5 TEP Riboswitch 5
Shift 7 x 5 TEP Riboswitch 5
Shift 5 x 5 TEP Riboswitch 3
Shift 6 x 5 TEP Riboswitch 3
Shift 7 x 5 TEP Riboswitch 3
Structure Competition 3x3 v1
Structure Competition 3x3 v2
Structure Competition 2x2 v1
Structure Competition 2x2 v2
Structure Competition 1x1 v1
Structure Competition 1x1 v2
Structure Competition 0x0 v1
Structure Competition 0x0 v2
TEP Aptamer Chemical Mapping Footprint
TEP Aptamer Chemical Mapping Footprint 2
TEP Aptamer Chemical Mapping Footprint 3
6.407
R93 R93.googlesheet
binary capture
Control II - Intermolecular KL
27.251
R94 R94.googlesheet
Three Branch Junction - AAAUAAA
Three Branch Junction - Sequence Mutation 1
Three Branch Junction - Sequence Mutation 2
Three Branch Junction - Sequence Mutation 3
Three Branch Junction - Structure Mutation 1
Three Branch Junction - Structure Mutation 2
External Loop Test
Hairpin Loop Test
Multibranch Loop Test
88-nt
72-nt
Lab Entry Level 0 - Chalk Outline lab revisited - Frozen shape with gap size 0
Lab Entry Level 0 - Chalk Outline lab revisited - Frozen shape with gap size 4
Lab Entry Level 1 - Chalk Outline lab revisited - Gap size 2
Lab Entry Level 2 - Chalk Outline lab modified - Gap size 2
Design your own Kissing-Loop
Control I - Parallel Crossover KL
Control II - Intermolecular KL
Six of One Mod
Solutions Aplenty by Mayanne
Pentaloop by Hyphema
Rational Design by ElNando888
Mod of Jandersonlee s Flip Turn 6-4 - Mark IV (split further) by Jieux
Collage by Hyphema
Slip Loop 5-4 by Jandersonlee
Straighten It 3 by Starryjess
Branch Zipper by codygeary
Can t Score This 6x6 by Jnicol
Mod of Barely Score This 6x5 by Jnicol
Mod of Cross Section by Starryjess
Mod of 1x1 Loop Experiment by Jieux
Lab Entry Level 0 - Tilted picture of running man revisited - Frozen shape with gap size 0
Lab Entry Level 0 - Tilted picture of running man revisited - Frozen shape with gap size 4
Lab Entry Level 1 - Tilted picture of running man revisited - Gap size 2
Lab Entry Level 2 - Tilted picture of running man modified - Gap size 2
GgaC/GgaC vs GagC/GagC 1
GgaC/GgaC vs GagC/GagC 2
GgaC/GgaC vs GagC/GagC 3
GgaC/GgaC vs GagC/GagC 4
GgaC/GgaC vs GagC/GagC 5
GgaC/GgaC vs GagC/GagC 6
GgaC/GgaC vs GagC/GagC 7
GgaC/GgaC vs GagC/GagC 8
GgaC/GgaC vs GagC/GagC 9
GgaC/GgaC vs GagC/GagC 10
GgaC/GgaC vs GagC/GagC 11
GgaC/GgaC vs GagC/GagC 12
GgaC/GgaC vs GagC/GagC 13
GagC/GagC vs GgaC/GgaC 1
GagC/GagC vs GgaC/GgaC 2
GagC/GagC vs GgaC/GgaC 3
GagG/CagC vs GgaG/CgaC
GgaG/CgaC vs GagG/CagC
GgaC/GgaC vs GagC/GagC 1B
GagC/GagC vs GgaC/GgaC 1B
 3.347
R95 R95.googlesheet
Lab Entry Level 0 - Water Strider revisited - Frozen shape with gap size 0
Lab Entry Level 0 - Water Strider revisited - Frozen shape with gap size 4
Lab Entry Level 1 - Water Strider revisited - Gap size 2
Lab Entry Level 2 - Water Strider modified - Gap size 2
5.067
R96

R96.googlesheet

R96.fusion table

Same State 1
Same State 2
Same State NG 1
Same State NG 2
Same State NG 3
Exclusion 1
Exclusion 2
Exclusion 3
Exclusion 4
Brourd's Mod of Exclusion 4
Exclusion 5
Exclusion 6
Sensor for hsa-mir-208a
Sensor v2, turn-off variant
Sensor v2, turn-off variant 2
Sensor v3, turn-off variant 1
Sensor v3, turn-off variant 2
 
R97

R97.googlesheet

R97.xlsx

R97.fusion table

R97ExclusionsWithDesignerAndLink.googlesheet

R97.Meechl's Exclusion Plus - Fusion Table

Most Recent Fusion Table for R97 (hopefully)

Brourd's Mod of Exclusion 4
Exclusion 1
Exclusion 2
Exclusion 3
Exclusion 4
Exclusion 5
Exclusion 6
Sensor, turn-off variant 1
 
 

R98 NG Fusion Table

   
       
R100 R100 google spreadsheet    
R101 R101 FMN MS2 Riboswitch Structure, with Switch Graphs    
R102    
R103 R103 Google spreadsheet    

 

Lab Data Resources

Players and developers have made valuable collections of lab data.

Signal to noise averages per lab by Meechl

Signal to noise averages per round by Meechl

Cloud Lab Data by Meechl

All Rounds by Meechl

List of past labs by Omei

All Rounds - All the data - Fusion table by Omei

Lab Summary - Round data by developers

Synthesized Labs - Lab data by developers

Das Lab Files by developers and Omei 

Comments on MS2 round 1 lab results by Salish99

MS2 Spreadsheet by Meechl

Fusion Table for MS2 Riboswitches on Chip (Round 1) by Omei

 

Fusion Table Resources

Intro To Fusion Tables by Eli Fisker

Variations On Maslow Design, Round 2 by Omei

Creating A Nearby Solutions Fusion Table by JandersonLee

 

See Also

Personal tools
Main page
Introduction to the Game