From 520d9a57c1786f78312ec1f689a583661a89acb8 Mon Sep 17 00:00:00 2001 From: Larry Du Date: Tue, 30 Mar 2021 10:24:48 -0700 Subject: [PATCH] Added linebreaks and cleaned up formatting. --- sequenced.md | 36 +++++++++++---- style.css | 121 +-------------------------------------------------- 2 files changed, 29 insertions(+), 128 deletions(-) diff --git a/sequenced.md b/sequenced.md index 43eaf25..f225a3d 100644 --- a/sequenced.md +++ b/sequenced.md @@ -15,8 +15,7 @@ the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence informationfor the RNA components of the initial -[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 +[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 reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any @@ -74,9 +73,8 @@ ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Marc Salit, Bijoyita Roy). -### Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b -vaccine. - Although the full coding region is included,the nature of the methodology used for +### Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine. +Although the full coding region is included,the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from @@ -91,9 +89,11 @@ This is a partial sequence of the vaccine RNA. Although the full coding region i assembled contig could lack some sequence from the ends of the RNA. + **Figure 1: Spike-encoding contig assembled from BioNTech/PfizerBNT-162b vaccine.** -GAGAATAAACTAGTATTCTTCTGGTCCCCACAGACTCAGAGAGAACCCGCCACCATGTTCGTGTTCCTGGTGCTGCTGCCTCTGGTGTCCAGCCAGTGTGTGAACCTGACCACCAGAACACAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCGACAAGGTGTT +GAGAATAAACTAGTATTCTTCTGGTCCCCACAGACTCAGAGAGAACCCGCCACCATGTTCGTGTTCCTGGTGCTGCTGCCTCTGGTGTCCA + GCCAGTGTGTGAACCTGACCACCAGAACACAGCTGCCTCCAGCCTACACCAACAGCTTTACCAGAGGCGTGTACTACCCCGACAAGGTGTT CAGATCCAGCGTGCTGCACTCTACCCAGGACCTGTTCCTGCCTTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGTCCGGCACC AATGGCACCAAGAGATTCGACAACCCCGTGCTGCCCTTCAACGACGGGGTGTACTTTGCCAGCACCGAGAAGTCCAACATCATCAGAGGCT GGATCTTCGGCACCACACTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAACAACGCCACCAACGTGGTCATCAAAGTGTGCGAGTTCCA @@ -127,21 +127,32 @@ TCGCCAACCAGTTCAACAGCGCCATCGGCAAGATCCAGGACAGCCTGAGCAGCACAGCAAGCGCCCTGGGAAAGCTGCAG CCAGAATGCCCAGGCACTGAACACCCTGGTCAAGCAGCTGTCCTCCAACTTCGGCGCCATCAGCTCTGTGCTGAACGATATCCTGAGCAGA CTGGACCCTCCTGAGGCCGAGGTGCAGATCGACAGACTGATCACAGGCAGACTGCAGAGCCTCCAGACATACGTGACCCAGCAGCTGATCA GAGCCGCCGAGATTAGAGCCTCTGCCAATCTGGCCGCCACCAAGATGTCTGAGTGTGTGCTGGGCCAGAGCAAGAGAGTGGACTTTTGCGG -CAAGGGCTACCACCTGATGACTCGAGCTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCCTGGGTACCCCGAGTCTCCCCCGACCTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCCCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACCCTGGAGCTAGCA +CAAGGGCTACCACCTGATGACTCGAGCTGGTACTGCATGCACGCAATGCTAGCTGCCCCTTTCCCGTCC + TGGGTACCCCGAGTCTCCCCCGAC + CTCGGGTCCCAGGTATGCTCCCACCTCCACCTGCCCCACTCACCACCTCTGCTAGTTCCAGACACCTCCCAAGCACGCAGCAATGCAGCTCAA + AACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACACCCTGGAGCTAGCA Cyan: Putative 5’ UTR + Green: Start Codon + Yellow: Signal Peptide + Orange: Spike encoding region + Red: Stop codon(s) + Purple: 3’ UTR + Blue: Start of polyA region (incomplete) + **Figure 2: Spike-encoding contig assembled from Moderna mRNA-1273 vaccine.** -GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGACCCCGGCGCCGCCACCATGTTCGTGTTCCTGGTGCTGCTGCCCCTGGTGAGCAGCCAGTGCGTGAACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGACAAGGT +GGGAAATAAGAGAGAAAAGAAGAGTAAGAAGAAATATAAGACCCCGGCGCCGCCACCATGTTCGTGTTCCTGGTGCTGCTGCCCCTGGTGA + GCAGCCAGTGCGTGAACCTGACCACCCGGACCCAGCTGCCACCAGCCTACACCAACAGCTTCACCCGGGGCGTCTACTACCCCGACAAGGT GTTCCGGAGCAGCGTCCTGCACAGCACCCAGGACCTGTTCCTGCCCTTCTTCAGCAACGTGACCTGGTTCCACGCCATCCACGTGAGCGGC ACCAACGGCACCAAGCGGTTCGACAACCCCGTGCTGCCCTTCAACGACGGCGTGTACTTCGCCAGCACCGAGAAGAGCAACATCATCCGGG GCTGGATCTTCGGCACCACCCTGGACAGCAAGACCCAGAGCCTGCTGATCGTGAATAACGCCACCAACGTGGTGATCAAGGTGTGCGAGTT @@ -182,13 +193,20 @@ CAACACCGTGTACGATCCCCTGCAGCCCGAGCTGGACAGCTTCAAGGAGGAGCTGGACAAGTACTTCAAGAATCACACCA GACCTGGGCGACATCAGCGGCATCAACGCCAGCGTGGTGAACATCCAGAAGGAGATCGATCGGCTGAACGAGGTGGCCAAGAACCTGAACG AGAGCCTGATCGACCTGCAGGAGCTGGGCAAGTACGAGCAGTACATCAAGTGGCCCTGGTACATCTGGCTGGGCTTCATCGCCGGCCTGAT CGCCATCGTGATGGTGACCATCATGCTGTGCTGCATGACCAGCTGCTGCAGCTGCCTGAAGGGCTGTTGCAGCTGCGGCAGCTGCTGCAAG -TTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACCTGATAATAGGCTGGAGCCTCGGTGGCCTAGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCAAAAAAAAA +TTCGACGAGGACGACAGCGAGCCCGTGCTGAAGGGCGTGAAGCTGCACTACACCTGATAATAGGCTGGAGCCTCGGTGGCCTAGCTTCTTGCCC + CTTGGGCCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCAAAAAAAAA Cyan: Putative 5’ UTR + Green: Start Codon + Yellow: Signal Peptide + Orange: Spike encoding region + Red: Stop codon(s) + Purple: 3’ UTR + Blue: Start of polyA region (incomplete) diff --git a/style.css b/style.css index d6209ec..3d1f2ef 100644 --- a/style.css +++ b/style.css @@ -1,120 +1,3 @@ /* - * CSS for making a resume with pandoc. Inspired by moderncv. - * - * This CSS document is delivered to you under the CC BY-SA 3.0 License. - * https://creativecommons.org/licenses/by-sa/3.0/deed.en_US - */ - -/* Whole document */ -body { - font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; - width: 800px; - margin: auto; - background: #FFFFFF; - padding: 9px 9px 9px 9px; - font-size: 12px; -} - -/* Title of the resume */ -h1 { - font-size: 40px; - color: #446fff; - text-align:center; - margin-top: 4px; - margin-bottom:8px; -} -h1:hover { - color: #094fff; - text-shadow: 1px 1px 1px #333; -} - -/* Titles of categories */ -h2 { - color: #000000; - margin-bottom:3px; -} -h2:hover { - color: #094fff; - text-shadow: 1px 1px 1px #333; -} - -/* There is a bar just before each category */ -h2:before { - content: ""; - display: inline-block; - margin-right:1%; - width: 10%; - height: 10px; - background-color: #0936ff; -} -h3 { - color: #000000; - margin-bottom: 3px; -} - -h4 { - margin-bottom: 2px; -} - -h5{ - color: #989898; - margin-top: 2px; - margin-botton: 3px; - padding: 0px; -} - -/* Definitions */ -dl{ - margin-top: 5px; - margin-bottom: 10px; -} -dt { - float: left; - clear: left; - width: 17%; - margin-bottom: 25px; /*Space out these sections*/ - /*font-weight: bold;*/ -} -dd { - margin-left: 20%; -} -p { - margin-top:0; - margin-bottom:3px; -} - -/* Blockquotes */ -blockquote { - margin-top: 2px; - margin-bottom: 2px; - padding: 3px; - text-align: center; -} - -ul{ - padding-top: 1px; - padding-bottom: 1px; - margin-top: 0px; - padding-left: 4px; -} - -li{ - margin-top: 2px; -} - -/* Links */ -a { - text-decoration: none; - color: #001488; -} -a:hover, a:active { - background-color: #0084ff; - color: #FFFFFF; - text-decoration: none; - text-shadow: 1px 1px 1px #333; -} - -/* Horizontal separators */ -hr { - color: #A6A6A6; -} \ No newline at end of file + * Replace this with a stylesheet to change the appearance of the document +/