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163 votes
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Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Good observation! The 3' poly(A) tail is actually a very common feature of positive-strand RNA viruses, including coronaviruses and picornaviruses. For coronaviruses in particular, we know that the ...
Cody Gray - on strike's user avatar
49 votes
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Why does the FASTA sequence for coronavirus look like DNA, not RNA?

That is the correct sequence for 2019-nCov. Coronavirus is of course an RNA virus and in fact, to my knowledge, every RNA virus in Genbank is present as cDNA (AGCT, i.e. thydmine) and not RNA (AGCU, i....
M__'s user avatar
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32 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

This question is quite general, so I'm going to attempt to tie it back to bioinformatics. Background The tree for the current coronavirus is here, showing it is closely related to bat-coronavirus and ...
M__'s user avatar
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24 votes
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Is it possible for coronavirus or SARS to be synthetic?

The scenarios are impossible and would be laughable if they were not so serious. The evidence is in the phylogenetic trees. Its a bit like a crime scene when the forensics team investigate. We've done ...
M__'s user avatar
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21 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Some of the other answers here seem quite good; at the same time I think the core answer to the OP's question is maybe a bit hard to tease out of them, so I'd like to try to state it more plainly. It'...
Zoë Sparks's user avatar
16 votes
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What reasons are there to choose Illumina if PacBio provides longer and better reads?

There are so many reasons why one might want to prefer Illumina over PacBio (also note that it's a false dichotomy, at least Oxford Nanopore is a competitive sequencing platform): The first (IMHO and ...
16 votes
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What is 'k' in sequencing?

See IUPAC codes: So, as you can see above, K means "Either G or T".
user6690's user avatar
  • 196
13 votes

Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

Not an expert, but some searching on eukaryotic positive-strand RNA viruses seems to show that polyadenylation is not uncommon. For example, Steil, et al., 2010.
merv's user avatar
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11 votes

How do I generate a color-coded tanglegram?

I think you can try dendextend, in this manual there is an example of coloring the branches. I don't think it is exactly like your coloring, but with a little tweaking you might get your colorscheme ...
benn's user avatar
  • 3,571
11 votes
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What is the best method to estimate a phylogenetic tree from a large dataset of >1000 loci and >100 species

This paper claims that FastTree is almost as accurate as RAxML, while being much faster. You just have to be careful, however, that the support values output by FastTree are not bootstrap values, they ...
Leo Martins's user avatar
11 votes
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A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

UPDATE: The article has now been withdrawn with the following note: This paper has been withdrawn by its authors. They intend to revise it in response to comments received from the research ...
Chris_Rands's user avatar
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8 votes

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

It seems to be explained right there in the image you posted: So, the three strains were classified based on three specific variants: Strain S, variant ORF8-L84S: a variant in the gene "ORF8&...
terdon's user avatar
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7 votes

How to create Phylogenetic Trees from fasta files in Python or R?

I would not look for a package for this, but instead build a small pipeline calling external tools with something like the following workflow: Cluster the ~100 sequences with CD-HIT-EST/PSI-CD-HIT or ...
Chris_Rands's user avatar
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7 votes

A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

Normally "inserts" used in the manuscript are "indels" in protein alignments, short for insertions and deletions. What I think has happened is a group investigating indels in HIV env noticed indels ...
M__'s user avatar
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7 votes

How can I add a ";" at the end of each fasta header line in a file?

One way, using sed and a regex address to select only the header lines and apply a substitution to append a semicolon to the end of each line: ...
Steve's user avatar
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6 votes
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Are phylogenetic tree construction algorithms any different than general clustering algorithms?

The goal of a phylogeny is to estimate the "expected" number of mutations between all taxa in the analysis and their hypothetical common ancestors. A cluster-analysis will only identify the "observed" ...
M__'s user avatar
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6 votes
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What are the different kinds of bioluminescent genes?

There are three processes wherein light is emitted. Bioluminescence: a chemical reaction releases light. The enzyme that does this is luciferase, while its substrate is luciferin, a small molecule. ...
Matteo Ferla's user avatar
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6 votes

What is the origin of HIV1?

They are both lentiviruses and share a distant common ancestor. HIV-1 and HIV-2 are descendents from simian immunodeficiency virus (SIV). The following tree shows the relationships very clearly, from ...
M__'s user avatar
  • 12.5k
6 votes

How can I add a ";" at the end of each fasta header line in a file?

... using the legendary Perl pie perl -p -i -e 's/^(>.*)/$1;/' mybacteria.fa Input ...
M__'s user avatar
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5 votes
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What is the best way to account for GC-content shift while constructing nucleotide-based phylogenetic tree?

There are models that take into account compositional heterogeneity both under the maximum likelihood and Bayesian frameworks. Although the substitution process is not time-reversible, the ...
Leo Martins's user avatar
5 votes

What reasons are there to choose Illumina if PacBio provides longer and better reads?

Many analyses performed on Illumina machines these days require large numbers of reads. For example, most analyses in ChIP-seq, RNA-seq, ATAC-seq etc, need 10s or even 100s of millions of reads for ...
Ian Sudbery's user avatar
  • 3,321
5 votes

Python - Finding a motif - input: a txt file with 10 sequences and 10 motifs

Let's start by doing some explaining about why your code doesn't work. ...
d_kennetz's user avatar
  • 631
5 votes

Are phylogenetic tree construction algorithms any different than general clustering algorithms?

A great question, though a little ambiguous. I don't know what "general clustering algorithms" refer to. For biological sequences, building a tree can be thought as a way of clustering. Anyway... ...
user172818's user avatar
  • 6,535
5 votes
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What does PCA mean on GWAS

From my memory of what a statistician told me, a PCA aims to determine independent linear combinations of variables (i.e. genotypes) that account for the most variation in the dataset. With 10 million ...
gringer's user avatar
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5 votes
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Ancestry of the coronavirus 2019-nCov, WuHan city, China

Overview The central focus of the tree is to highlight the key biological concern of the new coronavirus, 2019-nCov. The key concern is the genetic similarities to SARS epidemic, and relates to the ...
M__'s user avatar
  • 12.5k
5 votes

Why does the FASTA sequence for coronavirus look like DNA, not RNA?

If this were [cDNA], the end of the true mRNA sequence would be ...UCUUACUGUUUUUUUUUUUU, or a "poly(U)" tail. A cDNA sequence, maybe confusingly, refers to the coding strand of the cDNA (despite ...
Konrad Rudolph's user avatar
5 votes

Algorithmic investigation of viral proteins for vaccine design

There isn't a vaccine for any coronavirus, and your question is generally about targeted attentuation, which is a complex area. The basic building blocks for any vaccine development is virological ...
M__'s user avatar
  • 12.5k
4 votes

Counting letters in phylip alignment columns with Biopython

using something like for col in column(alignment): I may get the number of columns which have all the same letters (amino acids) ...
heathobrien's user avatar
  • 1,816
4 votes
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What is a site in a phylogenetic tree?

A site is simply an individual discrete position, normally a single nucleotide (or amino acid). For example, consider a toy alignment: ...
Chris_Rands's user avatar
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