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Questions tagged [sars-cov-2]

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4 votes
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SARS-CoV-2 sequence used in the AlphaSeq Antibody Datasets to predict binding affinity

Currently we are building a sequence based deep-learning model to predict binding affinity between antibody and antigen. For this we are training a sequence based model with AlphaSeq Antibody dataset (...
Krishna's user avatar
  • 43
1 vote
2 answers
134 views

How can I limit blast results to exclude a specific taxonomic ID?

I would like to perform blast+, using the command line, here is the code: -task blastn -db nr -outfmt 7 -query myQuery.fas -out result.txt -remote. I have to ...
Farzad Beikpour's user avatar
4 votes
1 answer
267 views

How to get a GISAID account? I registered months ago, still no reply!

Inspired by amateur variant hunters, I would like to join the Pango lineage proposal community and help contribute to variant surveillance. However, I cannot seem to get access to GISAID, the platform ...
AppleBees's user avatar
4 votes
1 answer
1k views

How to solve Nextflow error: "Trace file already exists"?

When trying to run epi2me-labs/wf-artic, I get the following error: ...
Cornelius Roemer's user avatar
2 votes
1 answer
76 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 ...
mac179's user avatar
  • 121
3 votes
1 answer
64 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
  • 12.5k
3 votes
4 answers
439 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
127 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
117 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
2 answers
95 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
5 votes
1 answer
89 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
102 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
2 votes
0 answers
38 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
201 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
57 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
  • 719
2 votes
1 answer
46 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
62 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
1 vote
1 answer
67 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
742 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
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 ...
Theo Jones's user avatar
1 vote
2 answers
461 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
63 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
  • 719
2 votes
2 answers
145 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
  • 719
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
1 answer
80 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
1 vote
1 answer
41 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
86 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
3 votes
2 answers
93 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
139 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, ...
Dare to ask-I dnt mind punishm's user avatar
0 votes
2 answers
730 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
0 votes
1 answer
115 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
115 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
141 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
2k 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
  • 1,804
3 votes
1 answer
62 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?
Dare to ask-I dnt mind punishm's user avatar
0 votes
1 answer
421 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
64 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
1 vote
0 answers
143 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 ...
Stanley Ho's user avatar
1 vote
0 answers
77 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 ...
Adrián P.L.'s user avatar
1 vote
1 answer
104 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: ...
greenpenguin's user avatar
2 votes
1 answer
62 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 ...
juanjo75es's user avatar
2 votes
1 answer
254 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. ...
juanjo75es's user avatar
1 vote
1 answer
2k 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 ...
virgiliocyte's user avatar
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 ...
yuval's user avatar
  • 141
8 votes
2 answers
197 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 ...
Vincent's user avatar
  • 181
3 votes
1 answer
581 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 ...
Lorenzo's user avatar
  • 41
3 votes
1 answer
173 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 ...
emonigma's user avatar
  • 133
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 ...
Roger V.'s user avatar
  • 381
1 vote
1 answer
520 views

What does the yellow mean in this image from Virus Pathogen Resource?

What does the yellow mean in this image of a SARS (coronavirus) protease from the Virus Pathogen resource database? It's from https://www.viprbrc.org/brc/
Andy's user avatar
  • 153
8 votes
1 answer
144 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 ...
Roger V.'s user avatar
  • 381