# Tag Info

147

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 poly(A) tail is required for replication, functioning in conjunction with the 3' untranslated region (UTR) as a cis-acting signal for negative strand synthesis ...

44

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.e. uracil). The reason is simple, we never sequence directly from RNA because RNA is too unstable and easily degraded by RNase. Instead the genome is reverse ...

31

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 in particular SARS. Question The bioinformatics question for the current coronavirus is why this virus appears to be able to infect humans and transmit to ...

24

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 enough crime-scenes often going to the site, collecting the pathogen, sequencing and then analysis - (usually neglected diseases) without any associated ...

20

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's worth noting that a truly complete answer to this question seems to be beyond current research, but any kind of "Why?" is inevitably a hard or even impossible ...

16

See IUPAC codes: So, as you can see above, K means "Either G or T".

16

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 to any sequencing experiment. Therefore the output is DNA and this is what NCBI provides here.

13

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.

11

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 in there. The manual mentions an argument called color_lines for the function tanglegram(): # The which parameter allows us to pick the elements in the list ...

11

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 are based on the Shimodaira-Hasegawa test. (Also, see this comment for the case you have very short branch lengths). [update: However, according to the ...

11

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 community on their technical approach and their interpretation of the results. If you have any questions, please contact the corresponding author. This is very ...

8

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): from ete3 import Tree, TreeStyle, faces def mylayout(node): if node.is_leaf(): logo_face = faces.ImgFace(str.split(node.name, '.')[0] + ".png") # this doesn't seem to work with eps files. You could ...

7

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 many other options Take all the sequences that form one individual cluster and build a multiple sequence alignment (MSA) with MAFFT/ClustalOmega or similar ...

7

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 in 2019-nCov. Essentially I think the correlation is spurious - but I haven't test it, but the area of research in understanding indels is certainly valid and ...

6

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 the organisms. Even "sequence" would be fine. Ninja edit to my own suggestion: since you're making a phylogeny from sequences of unknown context or relationship ...

6

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 SARS receptor. SARS background SARS is endemic in bats (your BioRxiv tree partly shows that and this tree definitely shows it) and in the 2002 epidemic infected ...

5

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 computations are simplified by assuming that the instantaneous rate matrix can be decomposed into an "equilibrium frequency vector" (non-homogeneous) and a symmetric, ...

5

No. A perfect phylogeny is one such that all characters evolve on the tree with no homoplasy, i.e. for a binary character, changes occur once from 0 -> 1 but never from 1 -> 0. A maximum parsimony phylogeny may produce a perfect phylogeny, but typically for real datasets some degree of homoplasy is required to explain character patterns.

5

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" mutations and "expected" and "observed" mutations can be majorly different due to the major artefact of reversion mutation. This is particularly true of ...

5

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 understanding of the proteins involved in pathogenesis. I will focus on covid-19 as an example here. The majority of bioinformatics work is based around the ...

5

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 Wertheim and Worobey (2009) Dating the Age of the SIV Lineages That Gave Rise to HIV-1 and HIV-2 PLoS Comp Biol. here. The evolution of HIV-1 is heavily mixed ...

4

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 creating a Neighbour Joining tree with MEGA, which is one of the simplest methods available. This should give you enough to check the relationships of the cultivars.

4

using something like for col in column(alignment): I may get the number of columns which have all the same letters (amino acids) len(set(col)) == 1 The number of columns which have at least 2 different amino acids (with no dashes): len(set(col)) > 1 and '-' not in col The number of columns which have any single dash: '-' in col or if you really ...

4

A site is simply an individual discrete position, normally a single nucleotide (or amino acid). For example, consider a toy alignment: sequence1 ATGC sequence2 ATCC # ^ arrow points to the third site Here there is 1 mutation in 4 sites, so 0.25 substitutions per nucleotide site. I'm not sure where the term originated, but probably one of the ...

4

snippy-core is a tool that processes the snippy_outdir_{1..n} folders and produces the following files: core.aln – a fasta format file that contains only the polymorphic sites (of {'A', 'C', 'T' and 'G'}) in your input set, whose length tends to decrease asymptotically as more isolates are added core.full.aln – a fasta format file that contains all the core ...

4

I finally managed to do it in R. Here is my code: install.packages('devtools') library(devtools) install_github('santiagosnchez/rBt') library(rBt) beast_output <- read.annot.beast('beast_output.trees') beast_output_rooted <- root.multiPhylo(beast_output, c('taxon_A', 'taxon_B')) unique_topologies <- unique.multiPhylo(beast_output_rooted) count &...

4

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 population genetics and the past, present and current population genetics distributions per population of HLA at http://www.allelefrequencies.net/

4

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... There are different tree building algorithms. Max parsimony (MP), max likelihood (ML) and bayesian algorithms directly take sequences as input. They are distinct ...

4

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 don't induce amino acid substitutions. Such mutations are commonly referred to as the third codon wobble, although occasionally the first codon can mutate and ...

4

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 files, e.g. due to too many chains. Presumably this is why the change was made, though mmCIF files tend to be larger and hence download slower. When calling save with the .pdb file extension the ...

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