All Questions
19 questions
1
vote
2
answers
143
views
Bio.codonalign.codonseq module (cal_dn_ds) for SARS-COV-2
I have calculated the dN,dS ratio for a SARS-COV-2 data set ('NC_045512.2' (Wuhan strain) and 'LC666924.1'), and results in a zero value (for most of the genes).
Is it possible and what is the ...
- 11
3
votes
1
answer
140
views
What is the origin of HIV1?
What is the origin of HIV1?
This is the alignment of a small part of the POL protein of the HIV1 virus GenBank KU749412.1, with the POL protein of the Visna virus GenBank L06906.1
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- 215
1
vote
0
answers
55
views
Comparison of phylogeny of SARS2 whole genome vs spike genome
I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files.
My next step is to compare the two phylogeny to look at if the mutations within SARS2 are more prevalent ...
- 75
3
votes
2
answers
305
views
Understanding the fasta file format and using edit distance for alignment
I'm a computer scientist teaching algorithms development in the Fall. One of the algorithms we teach is called Edit Distance, and our folklore is that it is used to compare RNA sequences (is this ...
- 131
4
votes
2
answers
1k
views
How can I classify the 3 clades(S, G, V) of the coronavirus without using protein data?
On GISAID they classified the coronavirus using 4 clades(S, G, V, Other).
I downloaded around 1,000 complete genomes of the coronavirus from GISAID and I would like to classify each one as belonging ...
- 141
3
votes
1
answer
587
views
Are the conclusions in "The proximal origin of SARS-CoV-2" legit?
I don't have any background in genetics and bioinformatics, so I ask you if you think that the arguments provided in the article The proximal origin of SARS-CoV-2 by Andersen et al. are convincing. In ...
- 41
3
votes
1
answer
103
views
Coronavirus phylogeny and evolution
This new article presents the phylogeny of the coronaviruses and the placement of the new coronavirus in it. This made me wonder of what we know about the coronavirus evolution, particularly where it ...
- 381
-1
votes
1
answer
158
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Algorithmic investigation of viral proteins for vaccine design [closed]
I wish to investigate how a virus could be attenuated through targeted mutagenesis by a priori prediction of attenuating amino acid mutations.
In particular, I am seeking bioinformatic solutions where ...
- 27
3
votes
1
answer
75
views
Practical use of RNA structure
I have spent some time studying RNA structures. While there is a range of interesting phenomena and functions that certainly deserve understanding from the scientific point of view, I have never ...
- 381
2
votes
1
answer
48
views
Database with antigens and current vaccines
I am seeking virological databases focussing on:
vaccines
antibody interactions
host receptors.
Preferably the data base will host multiple strains/samples of a given virus samples.
Any assistance ...
- 23
1
vote
1
answer
87
views
How can i get data set of illness and not illness people?
I'm reading a virology paper where the authors made a classification for the patients as to whether they had a specific disease outcome or not against the underlying sequence ...
The research focused ...
- 149
2
votes
2
answers
106
views
Detecting whether genome is genetically engineered?
Is there a methodology for detecting whether a genome has been tampered with by a biologist? For instance, say there has been an ebola outbreak such as in "The Andromeda Strain". Is there a way a ...
- 159
34
votes
4
answers
9k
views
Why does the FASTA sequence for coronavirus look like DNA, not RNA?
I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this:
...
- 443
20
votes
1
answer
2k
views
Is it possible for coronavirus or SARS to be synthetic?
I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...
- 313
9
votes
3
answers
2k
views
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?
Quote:
We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have ...
- 192
4
votes
1
answer
480
views
Interpretion of my coronavirus 2019-nCov, Wuhan, China BLAST tree?
This is the BLAST tree of the latest coronavirus out of China (from Wuhan Institute of Virology, China). It seems strange that there is so much divergence from all the other coronaviruses. Is this ...
- 41
5
votes
1
answer
905
views
Ancestry of the coronavirus 2019-nCov, WuHan city, China
In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus.
Can somebody assist a non-bio type here? It seems to show that the ...
- 153
191
votes
4
answers
124k
views
Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?
The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it...
...
- 1,725
3
votes
1
answer
137
views
Is there an R package that computes homoplasy excess ratios (HER)?
I want to calculate the homoplasy excess ratio for a phylogenetic tree, for example homoplasy resulting from recombination.
I am wondering if there are any R packages out there that will do this?
I ...
- 317