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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31 votes
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What is a quick way to find the reverse complement in bash

Thanks to Manu Tamminen for this solution: echo ACCTTGAAA | tr ACGTacgt TGCAtgca | rev
winni2k's user avatar
  • 2,256
30 votes
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Why sequence the human genome at 30x coverage?

The earliest mention of the 30x paradigm I could find is in the original Illumina whole-genome sequencing paper: Bentley, 2008. Specifically, in Figure 5, they show that most SNPs have been found, and ...
chrisamiller's user avatar
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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23 votes
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What is the fastest way to get the reverse complement of a DNA sequence in python?

I don't know if it's the fastest, but the following provides an approximately 10x speed up over your functions: ...
Devon Ryan'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
21 votes

Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done?

All humans have some differences in their DNA, but there's far more that is shared. On average the difference between humans is only about one thousandth of their full DNA, which means we're about 99....
curiousdannii's user avatar
18 votes
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Accuracy of the original human DNA datasets sequenced by Human Genome Project?

The HGP developed the first "reference" human genome - a genome that other genomes could be compared to, and was actually a composite of multiple human genome sequences. The standard human reference ...
kevbonham's user avatar
  • 298
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
Accepted

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
  • 651
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
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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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How to download FASTA sequences from NCBI using the terminal?

Alternatively, you can use the NCBI Entrez Direct UNIX E-utilities Basically, you have to download the install file here: https://www.ncbi.nlm.nih.gov/books/NBK179288/bin/install-edirect.sh In the ...
dc37's user avatar
  • 1,041
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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10 votes
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Importing GFF file with Biopython

No, there is currently no GFF support in biopython. However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like <...
conchoecia's user avatar
  • 3,141
10 votes

How to extract metadata from NCBI's short read archive (SRA) for a few runs?

Entrez Direct is perfect for this sort of thing. You can do something like this: ...
vkkodali's user avatar
  • 1,266
10 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.
Devon Ryan's user avatar
  • 19.6k
9 votes

What is the fastest way to get the reverse complement of a DNA sequence in python?

Here's a Cython approach that might suggest a generic approach to speeding up Python work. If you're manipulating (ASCII) character strings and performance is a design consideration, then C or Perl ...
Alex Reynolds's user avatar
9 votes

Theoretical limit of human genome compression

For the most modern CHM13 assembly (v2.0; Complete T2T reconstruction of a human genome; https://github.com/marbl/CHM13), the best known compression without any use of a reference is 567 MB (1.45 bits/...
Karel Břinda's user avatar
8 votes

Accuracy of the original human DNA datasets sequenced by Human Genome Project?

While the quality of the reference human assembly keeps improving, there are still misassemblies in it. A common problem is recent segmental duplications are occasionally collapsed into one sequence ...
user172818's user avatar
  • 6,525
8 votes
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Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first?

using a http request. if there is a DAS server, you can always use this protocol to download the xml -> fasta. see https://www.biostars.org/p/56/ ...
Pierre's user avatar
  • 1,511
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): ...
heathobrien's user avatar
  • 1,816
8 votes
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Why do these NCBI representative genomes for ape species have no Y chromosome?

tl;dr: technical difficulties, or sex For the gorilla, that genome is from a female gorilla (Kamilah the gorilla) so she doesn't have a Y chromosome. For the chimp link, there is a visualization of ...
Maximilian Press's user avatar
8 votes

Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done?

DNA is only the substance that makes up the genome. DNA can come with many forms. For example, the fragments you get by PCR in the lab are DNA. A bacterium also has DNA molecules in it. You may also ...
Phoenix Mu's user avatar
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
  • 9,901
7 votes

Why sequence the human genome at 30x coverage?

Solexa Inc. sequenced NA12878 chrX to ~30x in early 2007, which later became part of Bentley (2008). This, I believe, was the first time that 30x showed up. I don't recall they had a particular reason ...
user172818's user avatar
  • 6,525

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