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2 changes: 1 addition & 1 deletion topics/data-science/tutorials/gnmx-lecture6/tutorial.md
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> Image from [Pandas Docs](https://pandas.pydata.org/docs/getting_started/intro_tutorials/07_reshape_table_layout.html#wide-to-long-format).

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> Image from [Pandas Docs](https://pandas.pydata.org/docs/getting_started/intro_tutorials/07_reshape_table_layout.html#long-to-wide-table-format).

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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ it contains a variety of accessory proteins interspersed throughout the genome (
The long replicase gene encodes a number of non-structural proteins (nsps) and occupies 2/3 of the genome. Because of -1 ribosomal frameshifting within ORFab approx. in 25% of the cases
polyprotein pp1ab is produced in place of pp1a. pp1a encodes 11 nsps while pp1ab encodes 15 (Fig. below from [Sola:2015](https://www.annualreviews.org/doi/full/10.1146/annurev-virology-100114-055218)).

![Discontinuous transcription](https://www.annualreviews.org/na101/home/literatum/publisher/ar/journals/content/virology/2015/virology.2015.2.issue-1/annurev-virology-100114-055218/20151024/images/large/vi20265.f1.jpeg "Coronavirus genome structure and gene expression. (a) Coronavirus genome structure. The upper scheme represents the TGEV genome. Labels indicate gene names; L corresponds to the leader sequence. Also represented are the nsps derived from the processing of the pp1a and pp1ab polyproteins. PLP1, PLP2, and 3CL protease sites are depicted as inverted triangles with the corresponding color code of each protease. Dark gray rectangles represent transmembrane domains, and light gray rectangles indicate other functional domains. (b) Coronavirus genome strategy of sgmRNA expression. The upper scheme represents the TGEV genome. Short lines represent the nested set of sgmRNAs, each containing a common leader sequence (black) and a specific gene to be translated (dark gray). (c) Key elements in coronavirus transcription. A TRS precedes each gene (TRS-B) and includes the core sequence (CS-B) and variable 5′ and 3′ flanking sequences. The TRS of the leader (TRS-L), containing the core sequence (CS-L), is present at the 5′ end of the genome, in an exposed location (orange box in the TRS-L loop). Discontinuous transcription occurs during the synthesis of the negative-strand RNA (light blue), when the copy of the TRS-B hybridizes with the TRS-L. Dotted lines indicate the complementarity between positive-strand and negative-strand RNA sequences. Abbreviations: EndoU, endonuclease; ExoN, exonuclease; HEL, helicase; MTase, methyltransferase (green, N7-methyltransferase; dark purple, 2′-O-methyltransferase); nsp, nonstructural protein; PLP, papain-like protease; RdRp, RNA-dependent RNA polymerase; sgmRNA, subgenomic RNA; TGEV, transmissible gastroenteritis virus; TRS, transcription-regulating sequence; UTR, untranslated region.")
![Discontinuous transcription](https://www.annualreviews.org/docserver/fulltext/virology/2/1/vi20265.f1.gif "Coronavirus genome structure and gene expression. (a) Coronavirus genome structure. The upper scheme represents the TGEV genome. Labels indicate gene names; L corresponds to the leader sequence. Also represented are the nsps derived from the processing of the pp1a and pp1ab polyproteins. PLP1, PLP2, and 3CL protease sites are depicted as inverted triangles with the corresponding color code of each protease. Dark gray rectangles represent transmembrane domains, and light gray rectangles indicate other functional domains. (b) Coronavirus genome strategy of sgmRNA expression. The upper scheme represents the TGEV genome. Short lines represent the nested set of sgmRNAs, each containing a common leader sequence (black) and a specific gene to be translated (dark gray). (c) Key elements in coronavirus transcription. A TRS precedes each gene (TRS-B) and includes the core sequence (CS-B) and variable 5′ and 3′ flanking sequences. The TRS of the leader (TRS-L), containing the core sequence (CS-L), is present at the 5′ end of the genome, in an exposed location (orange box in the TRS-L loop). Discontinuous transcription occurs during the synthesis of the negative-strand RNA (light blue), when the copy of the TRS-B hybridizes with the TRS-L. Dotted lines indicate the complementarity between positive-strand and negative-strand RNA sequences. Abbreviations: EndoU, endonuclease; ExoN, exonuclease; HEL, helicase; MTase, methyltransferase (green, N7-methyltransferase; dark purple, 2′-O-methyltransferase); nsp, nonstructural protein; PLP, papain-like protease; RdRp, RNA-dependent RNA polymerase; sgmRNA, subgenomic RNA; TGEV, transmissible gastroenteritis virus; TRS, transcription-regulating sequence; UTR, untranslated region.")

## Virion structure

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