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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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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  • 7,062
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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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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  • 7,062
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
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Publicly available genome sequence database for viruses?

There area few different influenza virus database resources: The Influenza Research Database (IRD) (a.k.a FluDB - based upon URL) A NIAID Bioinformatics Resource Center or BRC which highly curates ...
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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
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
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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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11 votes

Why does the SARS-Cov2 genome has letter t

We sequence and therefore typically report assemblies as DNA sequences, even if they're actually RNA.
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10 votes
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What is deep sequencing?

I found a post useful for this topic. It explains the difference of coverage and depth. It also has a useful explanation on how to calculate coverage and depth. Here is a copy of what the link says ...
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9 votes

What is deep sequencing?

There are several questions in your post I'll try to answer each one: Is there any way to calculate how deep the sequencing is ? See gringer's answer. TLDR: The depth of the sequencing is how many ...
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  • 4,622
8 votes

What is deep sequencing?

Sequencing depth is typically calculated as the number of total bases sequenced divided by the number of bases in the target genome. An Illumina sequencing run with 2x125 bp reads and 500 million read ...
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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 ...
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  • 7,062
7 votes
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What does the yellow mean in this image from Virus Pathogen Resource?

Sulfur atoms are shown in yellow. The molecular viewer that you use is JSMol (JMol ported to the web). Atoms are colored by element: grey C, blue N, red O and yellow S. If you wonder how other atoms ...
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7 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&...
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  • 7,957
6 votes

Frequency of specific viral sequence in .BAM or .fastq

Most read aligners will report unaligned reads as well, which presumably will include your viral sequences. I would ask them to formally confirm that the BAM files will contain unaligned reads before ...
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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 ...
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  • 7,062
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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  • 7,062
5 votes

Economist article on coronavirus

R is a reference to R0, otherwise known as the basic reproductive rate, and means the number of new cases from a single patient infection. R0 has to be above 1 for a disease to persist. It is a ...
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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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5 votes

Understanding some of the computational bottlenecks of Covid-19 research

I can only speak of drug design (and even then I am terrible at turning down the jargon). In the case of drug design, this is pretty much plan C. Namely, none of compounds that entered clinical trial ...
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4 votes

Which sequence alignment tools support codon alignment?

I don't know of any transcript-to-transcript aligners that are able to do this, but LAST can align transcript queries to protein reference sequences using a specified frameshift cost. Here's the ...
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4 votes

Publicly available genome sequence database for viruses?

In addition to what others have suggested, I would also recommend PaVE as a resource. This is a curated database maintained by the NIAID and current holds over 300 papilloma virus genomes.
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4 votes

Viral genome assembly using broad viral ngs pipeline?

Since you are already using the Broad Tools sets you can use Picard FastqToSam to make the conversion As far a clipDb I am unfamiliar with that and a quick google search and look at the trimmomatic ...
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4 votes

Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?

The evolutionary related group (clade) of betacoronaviruses you have identified share an amino acid homology of 85% and include SARS. I know this from the underlying tree published on BioRxiv of a ...
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  • 7,062
4 votes
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Calculating the mortality rate of a pandemic, e.g. coronavirus 2019-nCov?

This may not strike most as a bioinformatics, but getting the key clinical outcome is essential in understanding the molecular basis of pathogenicity. I think the mortality rate is over-reported. ...
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4 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 ...
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4 votes
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Are the conclusions in "The proximal origin of SARS-CoV-2" legit?

In summary, the authors are saying the complete opposite of "human intervention". While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses ...
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  • 7,062
4 votes

Concerning the current outbreak, using bioinformatics

My personal approach to something like this is to first try to reproduce existing work in order to learn to use relevant tools and understand the concepts involved. Then as you get more comfortable ...
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