Lab

From Eterna Wiki

Revision as of 07:08, 8 August 2014 by Eli Fisker (talk | contribs) (Adding RMDB links)

This article is an overview of the RNA lab. For the lab FAQ, click here 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.

 

Introduction

In lab puzzles, players are presented with an target structure which must be solved. Each player may submit three lab designs and vote per round. Once submitted, the player's design is reviewed by other players, and voted on. The EteRNA team then synthesizes the most popular designs and performs experiments to determines their secondary structure and other chemical properties.

 

Lab Format

Target Structures

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.

 

Schedule

Labs are organized 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.

 

Voting and Submission

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.

 

Scoring

Lab designs are 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 <a title="SHAPE" href="/wiki/index.php5/SHAPE">SHAPE</a> 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 <a title="SHAPE" href="/wiki/index.php5/SHAPE">SHAPE</a> data for each base may be viewed by turning on the game option: "Use continuous colors for the exp. data".

 

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)


<tbody> </tbody>
Round  Comments Labs 
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R00_0000/ETERNA_R00_0000.rdat">R0</a><a href="https://docs.google.com/document/d/1ga8v6GoJxuHcs0LwNkljOLXX9VZWZLwsZmfWJfseYhA/edit"></a>

 

First batch of Player Projects

 

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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R00_0001/ETERNA_R00_0001.rdat">R1</a>

Second batch of Player Projects

Tested with four different SHAPE reagents:

  • NMIA
  • DMS
  • CMCT
  • 1M7

Signal-to-Noise Averages not currently available  

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R00_0002/ETERNA_R00_0002.rdat">R2</a>

Third batch of Player Projects

Tested with four different SHAPE reagents:

  • NMIA
  • DMS
  • CMCT
  • 1M7

Each design was tested with each reagent twice, the second time with a different barcode

Signal-to-Noise Averages not currently available 


<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R69_0000/ETERNA_R69_0000.rdat">R69</a>  

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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R70_0000/ETERNA_R70_0000.rdat">R70</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R71_0000/ETERNA_R71_0000.rdat">R71</a>   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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R72_0000/ETERNA_R72_0000.rdat">R72</a>   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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R73_0000/ETERNA_R73_0000.rdat">R73</a>  

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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R73_0001/ETERNA_R73_0001.rdat">R73.0001</a>  
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R74_0000/ETERNA_R74_0000.rdat">R74</a>  

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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R75_0000/ETERNA_R75_0000.rdat">R75</a>    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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R76_0000/ETERNA_R76_0000.rdat">R76</a>    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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R76_0001/ETERNA_R76_0001.rdat">R76.0001</a>  
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R77_0000/ETERNA_R77_0000.rdat">R77</a>   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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R78_0000/ETERNA_R78_0000.rdat">R78</a>  

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

Reproducibility Lab Another Round - Shape 7

Reproducibility Lab Another Round - Shape 8

Reproducibility Lab Another Round - Shape 9

Reproducibility Lab Another Round - Shape 10

Reproducibility Lab Another Round - Shape 11

Reproducibility Lab Another Round - Shape 12

Reproducibility Lab Another Round - Shape 13

Reproducibility Lab Another Round - Shape 14

Reproducibility Lab Another Round - Shape 15

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

<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R79_0000/ETERNA_R79_0000.rdat">R79</a>    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

CR4-5 domain of human telomerase - Shape 15

CR4-5 domain of human telomerase - Shape 16

CR4-5 domain of human telomerase - Shape 17

CR4-5 domain of human telomerase - Shape 18

CR4-5 domain of human telomerase - Shape 19

CR4-5 domain of human telomerase - Shape 20

CR4-5 domain of human telomerase - Shape 21

CR4-5 domain of human telomerase - Shape 22

CR4-5 domain of human telomerase - Shape 23

CR4-5 domain of human telomerase - Shape 24

CR4-5 domain of human telomerase - Shape 25

CR4-5 domain of human telomerase - Shape 26

CR4-5 domain of human telomerase - Shape 27

CR4-5 domain of human telomerase - Shape 28

CR4-5 domain of human telomerase - Shape 29

CR4-5 domain of human telomerase - Shape 30

CR4-5 domain of human telomerase - Shape 31

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CR4-5 domain of human telomerase - Shape 36

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CR4-5 domain of human telomerase - Shape 38

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

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<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R80_0000/ETERNA_R80_0000.rdat">R80</a>   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

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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

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<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R81_0000/ETERNA_R81_0000.rdat">R81</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R82_0000/ETERNA_R82_0000.rdat">R82</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R83_0000/ETERNA_R83_0000.rdat">R83</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R83_0002/ETERNA_R83_0002.rdat">R83.0002</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R83_0003/ETERNA_R83_0003.rdat">R83.0003</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R84_0000/ETERNA_R84_0000.rdat">R84</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R85_0000/ETERNA_R85_0000.rdat">R85</a>    
<a href="http://rmdb.stanford.edu/site_media/rdat_files/ETERNA_R86_0000/ETERNA_R86_0000.rdat">R86</a>    

 

You can get an idea about the average error rate for a lab here. 

<a href="https://docs.google.com/spreadsheets/d/16D7h8pY_tqPnegawl1puDkwjNOtFR8FDrPmE-eNKF4Q/edit#gid=1636220653">Signal to noise averages</a> by Meechl

 

==See Also==