Questions tagged [covid-19]
The covid-19 tag has no usage guidance.
49
questions
0
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1answer
38 views
Rejected publication [closed]
A publication that we have been working on for over 6 months on COVID-19 has been rejected by 2 journals. The objective of our research was to identify effective compounds against the COVID-19 virus ...
1
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1answer
36 views
Why ORF13 and ORF14 of Bat Sars coronavirus Rp3 have no corrispondence in Sars2?
Here I'am comparing bats coronavirus with Sars2, i.e. COVID-19. I have one question... Here result that one Bat Sars
coronaviurs identify in GenBank as DQ071615.1 has the ORF13(28122..28415) and ORF14(...
0
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2answers
29 views
How to count the kmer occurrence in FASTA file considering overlapping and reverse complement?
I am using count_overlap() for counting the kmers from Biopython .
Does it take the reverse complement of kmer into account?
I need to count reverse complement too
1
vote
0answers
22 views
Comparison of phylogeny of SARS2 whole genome vs spike genome
This is more of a general bioinformatics question, not any coding required.
So I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files.
My next step is to compare ...
1
vote
2answers
35 views
Why does Coronavirus genome contain poly A region at the 3' end in GenBank? [duplicate]
If you look at the Coronavirus genome below, it contains poly-A region at the end. I know that the viral RNA contains a poly-A tail. But, the genome in GenBank is stored in cDNA format. That means the ...
2
votes
1answer
15 views
mRNA cap identification by sequencing?
If you sequence a positive-sense RNA virus genome using NGS via Nanopore, Illumina or even the old Sanger method, is it possible to tell if the virus has 5' (five prime) cap at the 5' end of the RNA ...
0
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0answers
31 views
How to get % similarity between strains and mutation files
I’m very new to python, and having some difficulty getting hang of some more complicated things
I have multiple files which look like so:
hCoV-19/Singapore/4/2020|EPI_ISL_410535|2020-02-03
hCoV-19/...
2
votes
1answer
59 views
Virus genome: protein inside another protein
The genome sequence for the GenBank virus JX869059.2 (a human betacoronavirus) contains, among others, two proteins: N protein (range 28566..29807) and Orf8b (range 28762..29100). The interval for ...
2
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1answer
39 views
COVID-19 GWAS: what is a cross-replicating association?
In a genomic study of patients infected with SARS-CoV-2, the authors detected cross-replicating associations with rs11385942 at locus 3p21.31 , the association signal spanned the genes SLC6A20, ...
0
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2answers
66 views
How to get transcriptome FASTA file for viruses for Kallisto pseudo-alignment?
I guess the title is self-explanatory. I'd like to find the reference transcriptome files for a few human viruses. My RNA-seq samples are from human tumor cells that were infected with viruses. The ...
1
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2answers
132 views
Understanding the fasta File Format
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 ...
0
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1answer
62 views
Identification of starting point for the synthesis of a protein
identify where is the starting point for the synthesis of a protein in the DNA
For indentify a starting point in RNA or DNA my function search all ATG or M in the sequece and report the linear ...
1
vote
1answer
45 views
Human Herpes Virus, fusion motif in protein vs. SARS-CoV-2?
Is it possible that the fusion with cell propriety of Human Herpes virus, I see X14112.1 in GenBank is due to protein UL36 (tegument of virus) starting in linear position 2685 ???
...
1
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1answer
29 views
Selecting part of an extracted ligand
I have the PDB 6LU7.
I extracted the ligand using extract lig, org and then the protein using extract prot, poly. The ligand has three parts: 02J, PJE, and 010.
I want to select the 02J and 010 ...
3
votes
1answer
34 views
Why is there a chloride ion in this 3D model?
Here we have a 3D model of a sequence that match with this sequence
VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK
in Blast
the 3D structure is here
Why is there a chloride ion in this 3D model?
0
votes
1answer
58 views
How to calculate mutation rate and mutation sites in a genome using FASTA file?
I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format.
How I can identify mutations and mutation sites in those genomes using FASTA sequences but how I can do ...
1
vote
1answer
36 views
Why does the Genbank phylogenetic tree of 4000 sars-cov-2 sequences only display 200 nodes?
I manually selected all 4000 sequences on the 20 pages of the SARS-CoV-2 sequences on genbank here.
When I click on Build phylogenetic tree, it only has 200 nodes.
...
1
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0answers
22 views
Alternatives to phrap for merging contigs with overlapping ends?
I have bins from metagenomes generated with metabat2 on bitbucket/berkleylab/scr which are predicted as viral by MARVEL. MARVEL ...
1
vote
0answers
46 views
Analyzing a blast result of NGS data
I am analyzing BLAST results from total RNA NGS, pair ends. This BLAST results was performed against the ssRNA virus database download from NCBI.
I filtered those read data whose paired ends ...
1
vote
1answer
55 views
Significance of k-mer length in COVID-19 sequence analysis?
I'm getting started in biology and bioinformatics with sequencing the SARS-Cov-2 or Coronavirus genome. I'm interested in this code which identifies k-mers in the genome:
...
2
votes
1answer
51 views
Assembly reads having a copy of their beginning in their tail
I am analyzing the reads for the SARS-CoV-2 assembly with id SRR11140748. Apparently these reads were obtained with parallel sequencing by Illumina and Oxford Nanopore Technologies.
I have found these ...
1
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1answer
71 views
What is the meaning of these misaligned reads in a sequencing run?
I guess that's a basic question but I can't find an answer.
I am analyzing some SARS-CoV-2 sequencing runs. I often find read alignments like the one in the image.
...
0
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2answers
115 views
Concerning the current outbreak, using bioinformatics [closed]
Dear Researches community
A question concerning the current outbreak, recently we attempting to contribute to the study of the Covid19, with a tight submission time ( 4 weeks).
Inquiring help ...
1
vote
1answer
65 views
Set new Idents based on gene expression in Seurat and mix n match identities to compare using FindAllMarkers
I am relatively new to Bioinformatics and scRNA-seq data analysis. I am using Seurat V3 to analyze a scRNA-seq dataset in R. Currently, I have merged three scRNA-seq samples from the same donor into ...
3
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2answers
964 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 ...
8
votes
2answers
158 views
Understanding some of the computational bottlenecks of Covid-19 research
I am a researcher in high-performance computing (with very little bioinformatics background), and I am trying to understand what are the current biggest computational bottlenecks of software used for ...
2
votes
1answer
341 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 ...
2
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1answer
155 views
Prediction model for spread of coronavirus
A previous thread on Bioinformatics StackExchange citing an article by the Economist which references a cartoon of predictive outcomes by the CDC (Economist article on coronavirus) suggests a model in ...
2
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1answer
87 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 ...
7
votes
1answer
130 views
Coronavirus RNA structures?
Is there anything known about the RNA structures of coronaviruses? More specifically - do they have any interesting known structures in the translatable region, like RRE of HIV or the double loops in ...
-2
votes
1answer
135 views
Algorithmic investigation of viral proteins for vaccine design [closed]
I wish to investigate how a virus could be attenuated through targeted mutagenesis by investigating its protein mutations in order to produce an efficacious vaccine. Are there examples where the ...
5
votes
2answers
201 views
Economist article on coronavirus
I am wondering about an article in the Economist here:
https://www.economist.com/briefing/2020/02/29/covid-19-is-now-in-50-countries-and-things-will-get-worse
There is a graph there
The explanation ...
1
vote
1answer
169 views
Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?
Hello I'm helping to develop a cloud docking tool for screening compounds, similar to Swissdock but with mass throughput and GPU optimizations.
Specifically helping screen existing drugs against ...
0
votes
1answer
77 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 ...
2
votes
1answer
83 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 ...
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5answers
8k 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:
...
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3answers
632 views
Calculating the mortality rate of a pandemic, e.g. coronavirus 2019-nCov?
When calculating how lethal a virus outbreak is, I've noticed that most sources use
CONFIRMED_DEATHS/CONFIRMED_INFECTIONS
However, given that there are only 2 ...
14
votes
1answer
1k 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 ...
10
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3answers
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 ...
4
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1answer
432 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 ...
5
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2answers
822 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 ...
159
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4answers
85k 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...
...
3
votes
2answers
204 views
Frequency of specific viral sequence in .BAM or .fastq
I was wondering if anyone had any experience 'counting' the frequency of a particular viral sequence in an individual's fastq sequence. So basically, counting the number of occurrences of a particular ...
3
votes
1answer
64 views
Viral genome finishing
I have assembled poxvirus genome using Ray. The assembly is good. Out of several thousand contigs I got, I was able to get one scaffold using Contiguator tool, which is about 90% of my genome. I have ...
2
votes
1answer
61 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?
1
vote
3answers
186 views
Genome scaffolding
I assembled a virus genome using Ray and got around 5000 contigs. Now I want to scaffold those contigs to get a full genome (I am aware of the fact that there might be some gaps).
I found one tool ...
10
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3answers
2k views
Which sequence alignment tools support codon alignment?
Sometimes it useful to perform a nucleotide protein coding gene sequence alignment based on codons, not on individual nucleotides. For example for further codon model analysis it is important to have ...
14
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3answers
901 views
Publicly available genome sequence database for viruses?
As a small introductory project, I want to compare genome sequences of different strains of influenza virus.
What are the publicly available databases of influenza virus gene/genome sequences?
28
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4answers
34k views
What is the difference between FASTA, FASTQ, and SAM file formats?
I'd like to learn the differences between 3 common formats such as FASTA, FASTQ and SAM. How they are different? Are there any benefits of using one over another?
Based on Wikipedia pages, I can't ...
