Lab
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)
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
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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:
Signal-to-Noise Averages not currently available |
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<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:
Each design was tested with each reagent twice, the second time with a different barcode Signal-to-Noise Averages not currently available |
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<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 |
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<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 |
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<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 |
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<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 |
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<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 |
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<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 |
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<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 |
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<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 |
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<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 |
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<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 CR4-5 domain of human telomerase - Shape 32 CR4-5 domain of human telomerase - Shape 33 CR4-5 domain of human telomerase - 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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 |
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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 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 |
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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==