163
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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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49
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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__♦
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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__♦
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24
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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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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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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
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13
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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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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 ...
- 3,571
11
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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
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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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8
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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&...
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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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7
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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?
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__♦
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7
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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:
...
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6
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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. ...
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6
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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__♦
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6
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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
...
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5
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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 ...
- 669
5
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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 ...
- 3,271
5
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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.
...
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5
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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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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 ...
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5
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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__♦
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5
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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 ...
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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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4
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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 ...
- 182
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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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4
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Accepted
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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