Questions tagged [coronavirus]

Large family of single stranded, positive sense RNA viruses comprising SARS and SARS-CoV-2 (COVID-19)

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How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?

On GISAID they classified the coronavirus using 4 clades(S, G, V, Other). I downloaded around 1,000 complete genomes of the coronavirus from GISAID and I would like to classify each one as belonging ...
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Virus genome: protein inside another protein

The genome sequence for the GenBank virus JX869059.2 (a human betacoronavirus) contains, among others, two proteins: N protein (range 28566..29807) and Orf8b (range 28762..29100). The interval for ...
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Understanding the fasta File Format

I'm a computer scientist teaching algorithms development in the Fall. One of the algorithms we teach is called Edit Distance, and our folklore is that it is used to compare RNA sequences (is this ...
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COVID-19 GWAS: what is a cross-replicating association?

In a genomic study of patients infected with SARS-CoV-2, the authors detected cross-replicating associations with rs11385942 at locus 3p21.31 , the association signal spanned the genes SLC6A20, ...
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1answer
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Human Herpes Virus, fusion motif in protein vs. SARS-CoV-2?

Is it possible that the fusion with cell propriety of Human Herpes virus, I see X14112.1 in GenBank is due to protein UL36 (tegument of virus) starting in linear position 2685 ??? ...
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Prediction model for spread of coronavirus

A previous thread on Bioinformatics StackExchange citing an article by the Economist which references a cartoon of predictive outcomes by the CDC (Economist article on coronavirus) suggests a model in ...
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1answer
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Why ORF13 and ORF14 of Bat Sars coronavirus Rp3 have no corrispondence in Sars2?

I'am comparing bats coronavirus with Sars2, i.e. COVID-19. I have one question... one Bat Sars coronaviurs identify in GenBank as DQ071615.1 has the ORF13(28122..28415) and ORF14(28572..28784) ...
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Why does Coronavirus genome contain poly A region at the 3' end in GenBank? [duplicate]

If you look at the Coronavirus genome below, it contains poly-A region at the end. I know that the viral RNA contains a poly-A tail. But, the genome in GenBank is stored in cDNA format. That means the ...