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sequenced.md
36
sequenced.md
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@ -15,8 +15,7 @@ the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly
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distributed RNA species in numerous human populations. Despite their ubiquity, sequences
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distributed RNA species in numerous human populations. Despite their ubiquity, sequences
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are not always available for such RNAs. Standard methods facilitate such sequencing. In this
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are not always available for such RNAs. Standard methods facilitate such sequencing. In this
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note, we provide experimental sequence informationfor the RNA components of the initial
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note, we provide experimental sequence informationfor the RNA components of the initial
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[Moderna](https://pubmed.ncbi.nlm.nih.gov/32756549/)and [Pfizer/BioNTech](https://pubmed.ncbi.nlm.nih.gov/33301246/)
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[Moderna](https://pubmed.ncbi.nlm.nih.gov/32756549/)and [Pfizer/BioNTech](https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously
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COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously
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reported sequence information for the latter RNA.
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reported sequence information for the latter RNA.
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Sharing of sequence information for broadly used therapeutics has the benefit of allowing any
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Sharing of sequence information for broadly used therapeutics has the benefit of allowing any
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@ -74,9 +73,8 @@ ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit
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Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David
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Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David
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Lipman, Marc Salit, Bijoyita Roy).
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Lipman, Marc Salit, Bijoyita Roy).
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### Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b
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### Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine.
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vaccine.
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Although the full coding region is included,the nature of the methodology used for
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Although the full coding region is included,the nature of the methodology used for
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sequencing and assembly is such that the assembled contig could lack some sequence from
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sequencing and assembly is such that the assembled contig could lack some sequence from
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the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a
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the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a
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perfect match to the corresponding sequence from documents available online derived from
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perfect match to the corresponding sequence from documents available online derived from
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@ -91,9 +89,11 @@ This is a partial sequence of the vaccine RNA. Although the full coding region i
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assembled contig could lack some sequence from the ends of the RNA.
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assembled contig could lack some sequence from the ends of the RNA.
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**Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine.**
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**Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine.**
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<span style="background-color:cyan">GAGAATAAACTAGTATTCTTCTGGTCCCCACAGACTCAGAGAGAACCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color:yellow">TTCGTGTTCCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTG</span><span style="background-color:orange">AACCTGACCACCAGAACACAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCGACAAGGTGTT
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<span style="background-color:cyan">GAGAATAAACTAGTATTCTTCTGGTCCCCACAGACTCAGAGAGAACCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color:yellow">TTCGTGTTCCTGGTGCTGCTGCCTCTGGTGTCCA
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GCCAGTGTGTG</span><span style="background-color:orange">AACCTGACCACCAGAACACAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCGACAAGGTGTT
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CAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACC
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CAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACC
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AATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCT
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AATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCT
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GGATCTTCGGCACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAGTTCCA
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GGATCTTCGGCACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAGTTCCA
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@ -127,21 +127,32 @@ TCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAGCAAGCGCCCTGGGAAAGCTGCAG
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CCAGAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCAACTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGA
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CCAGAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCAACTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGA
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CTGGACCCTCCTGAGGCCGAGGTGCAGATCGACAGACTGATCACAGGCAGACTGCAGAGCCTCCAGACATACGTGACCCAGCAGCTGATCA
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CTGGACCCTCCTGAGGCCGAGGTGCAGATCGACAGACTGATCACAGGCAGACTGCAGAGCCTCCAGACATACGTGACCCAGCAGCTGATCA
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GAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGG
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GAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGG
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CAAGGGCTACCACC</span><span style="background-color: red">TGATGA</span><span style="background-color: magenta">CTCGAGCTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCCCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACCCTGGAGCTAGC</span><span style="background-color:blue">A</blue>
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CAAGGGCTACCACC</span><span style="background-color: red">TGATGA</span><span style="background-color: magenta">CTCGAGCTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCC
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TGGGTACCCCGAGTCTCCCCCGAC
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CTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCCCAAGCACGCAGCAATGCAGCTCAA
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AACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACCCTGGAGCTAGC</span><span style="background-color:blue">A</blue>
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<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
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<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
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<span style="background-color: green">Green: Start Codon</span>
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<span style="background-color: green">Green: Start Codon</span>
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<span style="background-color: yellow">Yellow: Signal Peptide</span>
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<span style="background-color: yellow">Yellow: Signal Peptide</span>
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<span style="background-color: orange">Orange: Spike encoding region</span>
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<span style="background-color: orange">Orange: Spike encoding region</span>
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<span style="background-color: red">Red: Stop codon(s)</span>
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<span style="background-color: red">Red: Stop codon(s)</span>
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<span style="background-color: magenta">Purple: 3’ UTR</span>
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<span style="background-color: magenta">Purple: 3’ UTR</span>
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<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>
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<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>
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**Figure 2: Spike-encoding contig assembled from Moderna mRNA-1273 vaccine.**
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**Figure 2: Spike-encoding contig assembled from Moderna mRNA-1273 vaccine.**
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<span style="background-color: cyan">GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGACCCCGGCGCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color: yellow">TTCGTGTTCCTGGTGCTGCTGCCCCTGGTGAGCAGCCAGTGCGTG</span><span style="background-color: orange">AACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGACAAGGT
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<span style="background-color: cyan">GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGACCCCGGCGCCGCCACC</span><span style="background-color: green">ATG</span><span style="background-color: yellow">TTCGTGTTCCTGGTGCTGCTGCCCCTGGTGA
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GCAGCCAGTGCGTG</span><span style="background-color: orange">AACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGACAAGGT
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GTTCCGGAGCAGCGTCCTGCACAGCACCCAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGCGGC
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GTTCCGGAGCAGCGTCCTGCACAGCACCCAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGCGGC
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ACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTACTTCGCCAGCACCGAGAAGAGCAACATCATCCGGG
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ACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTACTTCGCCAGCACCGAGAAGAGCAACATCATCCGGG
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GCTGGATCTTCGGCACCACCCTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGCGAGTT
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GCTGGATCTTCGGCACCACCCTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGCGAGTT
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@ -182,13 +193,20 @@ CAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAGCTGGACAAGTACTTCAAGAATCACACCA
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GACCTGGGCGACATCAGCGGCATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAGAACCTGAACG
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GACCTGGGCGACATCAGCGGCATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAGAACCTGAACG
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AGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGAT
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AGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGAT
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CGCCATCGTGATGGTGACCATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGCAGCTGCTGCAAG
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CGCCATCGTGATGGTGACCATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGCAGCTGCTGCAAG
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TTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACC</span><span style="background-color: red">TGATAATAG</span><span style="background-color: magenta">GCTGGAGCCTCGGTGGCCTAGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCA</span><span style="background-color: blue">AAAAAAAA</span>
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TTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACC</span><span style="background-color: red">TGATAATAG</span><span style="background-color: magenta">GCTGGAGCCTCGGTGGCCTAGCTTCTTGCCC
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CTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCA</span><span style="background-color: blue">AAAAAAAA</span>
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<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
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<span style="background-color: cyan">Cyan: Putative 5’ UTR</span>
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<span style="background-color: green">Green: Start Codon</span>
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<span style="background-color: green">Green: Start Codon</span>
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<span style="background-color: yellow">Yellow: Signal Peptide</span>
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<span style="background-color: yellow">Yellow: Signal Peptide</span>
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<span style="background-color: orange">Orange: Spike encoding region</span>
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<span style="background-color: orange">Orange: Spike encoding region</span>
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<span style="background-color: red">Red: Stop codon(s)</span>
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<span style="background-color: red">Red: Stop codon(s)</span>
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<span style="background-color: magenta">Purple: 3’ UTR</span>
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<span style="background-color: magenta">Purple: 3’ UTR</span>
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<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>
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<span style="background-color: blue">Blue: Start of polyA region (incomplete)</span>
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121
style.css
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style.css
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@ -1,120 +1,3 @@
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/*
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/*
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* CSS for making a resume with pandoc. Inspired by moderncv.
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* Replace this with a stylesheet to change the appearance of the document
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*
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/
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* This CSS document is delivered to you under the CC BY-SA 3.0 License.
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* https://creativecommons.org/licenses/by-sa/3.0/deed.en_US
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*/
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/* Whole document */
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body {
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font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
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width: 800px;
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margin: auto;
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background: #FFFFFF;
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padding: 9px 9px 9px 9px;
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font-size: 12px;
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}
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/* Title of the resume */
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h1 {
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font-size: 40px;
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color: #446fff;
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text-align:center;
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margin-top: 4px;
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margin-bottom:8px;
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}
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h1:hover {
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color: #094fff;
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text-shadow: 1px 1px 1px #333;
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}
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/* Titles of categories */
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h2 {
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color: #000000;
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margin-bottom:3px;
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}
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h2:hover {
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color: #094fff;
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text-shadow: 1px 1px 1px #333;
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}
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/* There is a bar just before each category */
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h2:before {
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content: "";
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display: inline-block;
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margin-right:1%;
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width: 10%;
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height: 10px;
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background-color: #0936ff;
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}
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h3 {
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color: #000000;
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margin-bottom: 3px;
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}
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h4 {
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margin-bottom: 2px;
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}
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h5{
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color: #989898;
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margin-top: 2px;
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margin-botton: 3px;
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padding: 0px;
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}
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/* Definitions */
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dl{
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margin-top: 5px;
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margin-bottom: 10px;
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}
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dt {
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float: left;
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clear: left;
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width: 17%;
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margin-bottom: 25px; /*Space out these sections*/
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/*font-weight: bold;*/
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}
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dd {
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margin-left: 20%;
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}
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p {
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margin-top:0;
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margin-bottom:3px;
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}
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/* Blockquotes */
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blockquote {
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margin-top: 2px;
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margin-bottom: 2px;
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padding: 3px;
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text-align: center;
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}
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ul{
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padding-top: 1px;
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padding-bottom: 1px;
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margin-top: 0px;
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padding-left: 4px;
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}
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li{
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margin-top: 2px;
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}
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/* Links */
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a {
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text-decoration: none;
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color: #001488;
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}
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a:hover, a:active {
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background-color: #0084ff;
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color: #FFFFFF;
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text-decoration: none;
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text-shadow: 1px 1px 1px #333;
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}
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/* Horizontal separators */
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hr {
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color: #A6A6A6;
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}
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