Questions tagged [covid-19]

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4 votes
2 answers
166 views

relation between Illumina sequencing primer and viral sequences

Dealing whith a problematic sequencing run I found this over-represented sequence: GGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGGCGTCTTCTGCTTG It is clearly relate to the Illumina sequencing primer ...
mox's user avatar
  • 323
2 votes
1 answer
54 views

Is there a way to extract spike sequence from a Sars-CoV-2 complete genome (preferably in Python)?

I have a complete genome sequence of a Sars-CoV-2 variant, but I am only interested in the Spike sequence? I should note that I am not a biologist (nor bioinformatics). The complete genome looks like ...
Amine Chadi's user avatar
2 votes
1 answer
114 views

Caching and parallelization

Currently algorithmically developing a calculation for "co-dependent" mutation (quotation appropriate). The algorithm uses chunked biopython alignment objects which are parallelized. Aim One ...
M__'s user avatar
  • 10.2k
2 votes
1 answer
60 views

Taking too long to download metadata file (estimated size 30MB) from Covid-19 Data Portal

I am working on developing a tool to classify covid variants. So I am trying to download SARS-CoV-2 sequence data along with lineage annotation from Covid-19 Data Portal (I could not find a better ...
Rajesh M's user avatar
3 votes
1 answer
44 views

Metagenomics pipeline recommendations for short-read data

de novo metagenomics on viral NGS data is a hot-topic. On this site alone at least 4 specific algorithms have been used to identify multi-strain/multi-species for a given data set, however these do ...
M__'s user avatar
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2 votes
4 answers
249 views

How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?

I would like to download a number of SARS-CoV-2 fastas from NCBI/Genbank using a web endpoint. I looked on their website but it's confusing. I have the accession numbers, but can't figure out how to ...
Cornelius Roemer's user avatar
1 vote
2 answers
106 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 ...
Alex's user avatar
  • 11
2 votes
1 answer
86 views

Visualization of mutations in (part of) viral genome - existing tools?

I'm trying to visualize mutations in SARS-CoV-2 sequences, somewhat like it's done on outbreak.info: but for individual sequences, probably on the base of the vcf files generated by the ARTIC ...
KeyboardCat's user avatar
3 votes
3 answers
195 views

Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)

Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these? For the moment I ...
aechchiki's user avatar
  • 2,656
3 votes
2 answers
83 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 ...
Cornelius Roemer's user avatar
2 votes
1 answer
54 views

Demovir produces an empty output

I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir* for doing taxonomic annotations on my viral contigs. First, I installed all ...
Ernie Hsieh's user avatar
5 votes
1 answer
86 views

Why does the SARS-Cov2 genome has letter t [duplicate]

ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is part of the 5'UTR of genome of an RNA virus SARS-Cov-2. RNA contains letters ...
Pavel Pelan's user avatar
3 votes
2 answers
80 views

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

I need to retrieve COVID-19 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....
Sk Sarif Hassan's user avatar
3 votes
1 answer
63 views

Long-Covid (LC) GWAS project proposal: should I include a non-LC GWAS?

I am working on a project proposal for an exam, it involves a budget of 1M euros and I got to design a genomic study. I chose a GWAS to assess altered gene expression after covid19 that leads to long-...
fecke9296's user avatar
2 votes
0 answers
37 views

Why isn’t ace2 included in SARS‑CoV‑2 PPI map?

I'm doing my master's thesis on drug repositioning for SARS‑CoV‑2 using AI more specifically network medicine, I found only one human protein-protein interactions (PPIs) map from Gordon et al. The ...
hpPh's user avatar
  • 21
2 votes
1 answer
162 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 ...
juanjo75es's user avatar
2 votes
1 answer
357 views

Entrez (Biopython) esearch and efetch not returning sequence as expected

I'm trying to use Entrez (through Biopython) to download the sequence of a TMV replicase gene. I have the following code: ...
blammo69's user avatar
2 votes
1 answer
56 views

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

I have a fastq file from Nanopore sequencing data that contains reads from both the UK and South Africa variants of SARS-CoV-2. The variants are identified by three key mutations in the receptor-...
L R Joshi's user avatar
  • 709
2 votes
1 answer
43 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'...
Cornelius Roemer's user avatar
3 votes
2 answers
54 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 ...
S.J.A's user avatar
  • 31
3 votes
2 answers
81 views

Gold standard benchmark

This page is claimed to contain a gold standard benchmark for viral genome assembly. https://github.com/cbg-ethz/5-virus-mix The claim is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/ ...
juanjo75es's user avatar
3 votes
1 answer
134 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 ...
RosLuP's user avatar
  • 215
0 votes
1 answer
176 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 ...
ibio_rep1's user avatar
1 vote
1 answer
64 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) ...
RosLuP's user avatar
  • 215
1 vote
3 answers
530 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
Lipsa's user avatar
  • 21
1 vote
0 answers
53 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 ...
Theo Jones's user avatar
1 vote
2 answers
356 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: ...
Theo Jones's user avatar
1 vote
2 answers
58 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 ...
L R Joshi's user avatar
  • 709
2 votes
2 answers
96 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 ...
L R Joshi's user avatar
  • 709
1 vote
1 answer
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) ...
Theo Jones's user avatar
1 vote
2 answers
403 views

How to sort multiple FASTA files based on their content?

I have around 10,000 FASTA files of Influenza A virus. These files contains sequences of each of the 8 segments of the viral genome and I want to separate each genome segment into a different folder ...
Neeleshwar Pandey's user avatar
0 votes
2 answers
116 views

How to sort multiple FASTA files based on their content? [duplicate]

So I have around 10,000 FASTA files of Influenza A virus. These files contains sequences of each of the 8 segments of the viral genome and I want to separate these files into different locations based ...
Neeleshwar Pandey's user avatar
1 vote
1 answer
77 views

>My counter is counting genotypic combination occurences more than once, how do I ensure it counts one combination and doesnt count it again?

...
Theo Jones's user avatar
3 votes
3 answers
63 views

What is the typical host-to-bug DNA ratio found in nanopore sequencing without amplification?

I'm interested in sequencing a human sputum sample using an ONT MinION without performing any type of whole genome DNA amplification or targeted PCR. Has anyone found a good reference (or anecdotal ...
TimD1's user avatar
  • 282
1 vote
0 answers
84 views

UTR features in gbk files

I have a gbk files for a viral genome that I have used biopython to add features of the 3' and 5' ...
Lamma's user avatar
  • 143
1 vote
1 answer
40 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. ...
Theo Jones's user avatar
1 vote
1 answer
77 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/...
Theo Jones's user avatar
2 votes
2 answers
295 views

Genome assembly of SRR12196449 with SPAdes

I am trying to assemble the run SRR12196449 with SPAdes. The description of their project is: This project expected to standardize a method for amplification and ...
juanjo75es's user avatar
3 votes
2 answers
91 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 ...
RosLuP's user avatar
  • 215
2 votes
1 answer
126 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, ...
Milla's user avatar
  • 153
0 votes
1 answer
127 views

Resources to learn genome assembly workflow for small genomes (like viruses)

I have sequencing data of a few samples of a DNA virus. I'd like to learn de novo assembly of 'short read' data, to construct a scaffold and then count the abundance of each strain in the data. I ...
Reza Rezaei's user avatar
0 votes
2 answers
483 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 ...
Reza Rezaei's user avatar
3 votes
2 answers
241 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 ...
John's user avatar
  • 131
0 votes
1 answer
114 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 ...
RosLuP's user avatar
  • 215
2 votes
1 answer
113 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 ??? ...
RosLuP's user avatar
  • 215
1 vote
1 answer
89 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 ...
user8338's user avatar
2 votes
0 answers
1k 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 ...
kcm's user avatar
  • 1,694
3 votes
1 answer
51 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?
Milla's user avatar
  • 153
0 votes
1 answer
269 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 ...
Mendel's user avatar
  • 75
1 vote
1 answer
58 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. ...
Shadi's user avatar
  • 113