Questions tagged [sars-cov-2]

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1answer
34 views

How to convert Sars-CoV-2 ORF1ab codon positions to ORF1b positions?

Some websites mention amino acid mutations as ORF1ab, most however use ORF1a/b instead. So how can I translate from one to the other? What do I need to subtract from say ...
4
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1answer
67 views

Why does the SARS-Cov2 genome has letter t

ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is genome of an RNA virus SARS-Cov-2. RNA contains letters C+...
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1answer
23 views

Retrieval of metadata of a batch of 3953 sequence data from GISAID database

Can we retrieve metadata (such as date of collection of sequence data, location, etc.) for a batch of 3953 GISAID accessions from the GISAID database? I am not very comfortable with GISAID. I am more ...
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0answers
20 views

Why ace2 is not included in SARS-COV-2 PPIN map?

I'm doing my master's thesis on drug repositioning for sars-cov-2 using AI more specificaly network medicine, I found only one PPIN map from Gordon et al. but it doesn't include the ace2 protein which ...
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1answer
35 views

Consensus sequence from vcf file

I am generating a consensus sequence for SARS-Cov-2. I am visually inspecting every candidate SNP in a pileup. Sometimes I find that there are two consistent variants for the same position, but I can ...
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1answer
36 views

Detecting SARS-CoV-2 variants from the mixed virus population

I have a fastq file from Nanopore sequencing data that contains reads from the UK and South Africa variants of SARS-CoV-2. These variants are identified by three key mutations in the receptor-binding ...
2
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1answer
26 views

Python package or CLI tool outputting mutations of sequence with respect to reference

I'm new to bioinformatics, and I'm looking for a tool that takes two FASTA files, one containing a reference, let's call it A.fasta, the other another sequence, let'...
2
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2answers
39 views

Calling for one specific SNP from multiple sequencing runs

Just learning the basics of bioinformatics and bash shell scripting. Is there a correct way to search for a specific allele with one or even multiple sequencing runs? I am searching for prevalence of ...
4
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1answer
107 views

What origins for virus HIV1?

What origins for virus 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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1answer
56 views

Why ORF13 and ORF14 of Bat Sars coronavirus Rp3 have no corrispondence in Sars2?

I'am comparing bats coronavirus with Sars2, i.e. COVID-19. I have one question... one Bat Sars coronaviurs identify in GenBank as DQ071615.1 has the ORF13(28122..28415) and ORF14(28572..28784) ...
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3answers
173 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
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0answers
45 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 ...
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2answers
110 views

Extract sequences from MultiFASTA aligned file, by coordinates

I am trying to extract a specific sequence from a multifasta file, from each sequence in the aligned file. The sequences look like this, and there are 32 sequences within the multiFASTA: ...
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2answers
48 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
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2answers
54 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 ...
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1answer
52 views

Adding multiple dataframes to compare against genotypes - DATE/LOCATION - geotemporal incidences of SARS2 genotypes

I'm trying to reuse some code I have previously used to add extra parameters. In the initial code, it was used to give a 1/0 counter if a specific mutation was present (first code below) ...
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1answer
36 views

How to find Genotype, from list of mutations:lineage list?

I'm very new to python and I'm getting along nicely (I'd like to believe); however, I must be missing something here. I'm looking to read each and every file and compare each line against one another. ...
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1answer
65 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/...
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2answers
86 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
91 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, ...
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2answers
194 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 ...
2
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2answers
174 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 ...
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1answer
92 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 ...
2
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1answer
108 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 ??? ...
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1answer
41 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 ...
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0answers
277 views

Annotation label not matching to the color assigned in complex heatmap

The issue im facing is I'm assignig the colour to the annotation label but when it is rendered the label in my metadata does't match with the final output not sure what exactly is the problem. The ...
3
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1answer
40 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?
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1answer
128 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 ...
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1answer
49 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. ...
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0answers
45 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 ...
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0answers
57 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 ...
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1answer
75 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
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1answer
56 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 ...
2
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1answer
118 views

What is the meaning of these misaligned reads in a sequencing run?

I am analyzing some SARS-CoV-2 sequencing runs abd often find read alignments like the one in the image. ...
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1answer
325 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 ...
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2answers
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 ...
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2answers
183 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 ...
3
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1answer
545 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 ...
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1answer
162 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 ...
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1answer
98 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 ...
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1answer
137 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 ...
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1answer
149 views

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 ...
3
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1answer
57 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 ...
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2answers
203 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 ...
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1answer
431 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
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1answer
86 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 ...
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2answers
97 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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3answers
666 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 ...
4
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1answer
459 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 ...