Reproducibility Test Lab

 [http:  LabName] representative.
Round N. ID=[http: DesignID].
Score = NN.

The Reproducibilty Test Lab is a special lab that is (will be) synthesized in each synthesis round.  The objectives for this lab are:

• Provide a consistent measure of the reproducibilty of the cloud lab synthesis results, for long term quality control,
• Determine how much of the variation in synthesis results is captured by the error estimates reported for each synthesized base,
• Provide some guidance as to where the synthesis process might be improved, in order to increase reproducibility, and
• Give those analysing the synthesis data a better understanding of the variation to expect when comparing data from different synthesis rounds.

 

Initial Sequences

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Sequence	Description or rationale for inclusion	Original SHAPE data, or expected folding
AGUCAUCUAC UACGAAAAAC ACAUUCUAUU CGAAAACGAA UAGAAUGUGU CGUAGUAGAU GAC	Cloud Lab 1 representative. Round 1. ID=2366937. Score = 94.
GCAAGGACGA AUAAGCCAUA ACCGCAGGGA AACACUGAAC GGAGCCGAAA GAGCAAGCAA UAA	Cloud Lab 4 representative. Round 2. ID=2655773. Score = 88.
GAGAUGGGUA ACGAAAGUUG CGCUGCCGAA UGAAAGUUCU GGAUGAAAGU CUGGUGGCCU AUC	Cloud Lab 9 representative. Round 2. ID=2588792. Score = 78.  High GU content.
AGAGUGAAGG ACGGAGAAUC UCCGUCGUCG CGAAGCGGCC CUGGGCUUCC CAGGCUUCAC UCA	Cloud Lab 15 representative. Round 1. ID=2337872. Score = 96.
GAGAUAUUAU AAUAUUAUAA UAUGCAAAGA AAUAAGAAGC AUAUUAUAAU AUUAUAAUAU CAA	Cloud Lab 18 representative. Round 2. ID=2596919. Score = 98.  High AU count.
GCGGAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAC CGC	Clouud Lab 19 representative. Round 1. ID=2339041. Score = 92.  Big loop of all A.
GCGGCGGCAA AGGCGGCGCA ACGCGGCGGA AAAUCGGCGG CGACGCGGCG GAAAUCGGCG GCG	Cloud Lab 20 representative. Round 1. ID=2335964. Score = 91. Lab has lots of 1-1 loops.  Sequence is Christmas tree that scored well.
GUACAAAUCC UCGAAAACUC GAGGAUAUAU CAAAAGAUAG AAGGCGAGAA AAAAAGGAGG UAC	Hair Trigger representative. ID=2433439. From switch lab, with a similar estimated MFE between the two states (without aptamer.)
AAAAAGCUCC AUGAGGAUAU AGAGCAGAAA AUAUGCCUAG AAGGCAUGGU AAAAUAGCAA AAA	LS2 representative. ID=2435428. Switch lab.  Good scores in both states. State 1 not predicted to be MFE by Eterna energy model.
UAAGCACCAG GAGCAGGACC AGCGAAACAA AACAAACAAA GCAGGACCAG CACCAGGAGC AAA	Ball and Chain representative. ID=2763519. Score = 96.  Systematic testing of CG bases anchoring 1-1 loops with both As.
GAGCUAGUGC UGAGGAAACU UAGCCUAGCU CAGAUUUGCC UAAUCGAAAG AUUAGUGCAG AUC	RNA Bridge representative.  ID=3006655. Score = 77.  Good dot plot and melt plot, but low score.
	LabName representative. Round N. ID=SOLNNNN. Score = NN.
	LabName representative. Round N. ID=SOLNNNN. Score = NN.
GACGCCGAUG GUAGCAAGGG AAACCGAGGA AACUCGCGAA AGCAAAGCGA GAGUAGGAAA GUC	Huffman. ID=2736789. Score = 96. Sequence apperared to have stable stack including non-canconical pairs.
AGAGUGAAGG ACGCCGUUUC GGCGUCGUGC CCUUGGCACC CUCCCGAAGG GAGGCUUCAC UCA	Triloop Buffet. Round 2. ID=2676335. Score = 91. Sequence apperared to show tertiary bonding.
AUCGAAAGAU	Very short sequence
UAGCAGGGCUAGCUAGCUUGGCAAAAUUCGACGUAAGCAAAAUGCAAAAAACGUAUCGAUUAUAUUGAAAAAGAUCGGACUAGGCUAGG	Maximum length (89) sequence

 

rhiju → Omei:  please submit up to 40 sequences, this weekend if possible!

Omei → rhiju:  Will do. Am I correct in thinking that can refine the set over time, if we decide we would benefit from different sequences?

rhiju → Omei:  yes of course. I think we're granting you (and the players you represent) a 'standing order' of 40 sequences over each cycle to characterize errors and to make suggestions to us devs for viewing & experimental improvements. I'm excited to see what you find!