147 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 ...
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  • 1,336
46 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....
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  • 6,992
31 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 ...
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  • 6,992
25 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 ...
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  • 6,992
20 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'...
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17 votes

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

Most sequencing experiments, be it Illumina-based next-generation-sequencing or Sanger sequencing uses DNA as template, not RNA. Even if this virus is RNA-based it would be reverse-transcribed prior ...
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  • 2,706
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".
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  • 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.
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  • 541
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 ...
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  • 3,521
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 ...
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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 ...
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  • 3,462
8 votes
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Biopython Phylogenetic Tree replace branch tip labels by sequence logos

To expand on my comment from yesterday. You could do this with the ETE Toolkit (I just copied one logo file rather than converting all 26 to png): ...
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  • 1,806
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 ...
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  • 3,462
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 ...
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  • 6,992
6 votes
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Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?

Phylogenies can be made with/of non-species groups. I think "taxon" is perfectly fine. You might also consider the use of the "leaf / leaves" or "terminal" if you want to emphasise the tip nature of ...
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  • 758
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 ...
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  • 6,992
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 ...
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5 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" ...
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  • 6,992
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 ...
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  • 6,992
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 ...
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  • 6,992
5 votes
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How to get the number of complete phage genomes available on ncbi?

Go to the NCBI nuccore database, at https://www.ncbi.nlm.nih.gov/nuccore Copy and paste the search term: ...
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  • 6,992
4 votes

How does one construct a cladogram of intraspecies relationships?

Even with inbreeding and other genetic phenomena that might mask actual evolution of these cultivars, any phylogenetic methodology would be capable of determining relationships accurately. Try ...
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  • 182
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) ...
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  • 1,806
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: ...
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  • 3,462
4 votes

Does the ".full.aln" file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?

snippy-core is a tool that processes the snippy_outdir_{1..n} folders and produces the following files: ...
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4 votes
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Calculate the percentage of each unique phylogenetic tree in a BEAST output

I finally managed to do it in R. Here is my code: ...
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  • 191
4 votes

How to interpret UniProt allele patterns?

These are cytotoxic T-cell HLA alleles. HLA genotyping is very common and easy to do, so Genbank is the repository. A*11:01 has very high frequency in Aborigine populations here . You can explore the ...
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  • 6,992
4 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... ...
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  • 5,645
4 votes

For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?

For a species complex nucleotide phylogenies all the way. The reason is neutral mutation, which is not observed at the amino acid level because these mutations are part of the degenerate code which ...
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  • 6,992
4 votes
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PDB file downloading: pymol automation vs. manual

To expand on the comment by marcin: fetch downloads files in mmCIF format by default (https://pymolwiki.org/index.php/Fetch). Not all PDB entries have PDB format ...
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