Questions tagged [virus]

Biological kingdom of 'microparasite' that is unable to replicate without hijacking the hosts replication machinery

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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 ...
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How to use GEO_SPHERE?

I have some problems with geosphere package which extends/applies the Beast Bayesian MCMC package for calculating phylogenetic trees. Please, could anyone give any hints about at least one of them? ...
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How to get the number of complete phage genomes available on ncbi?

I am looking to establish the total number of complete phage genomes available on NCBI. I am not looking for any specific type, but want to understand the total diversity available. How can I perform ...
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1 answer
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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 ...
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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: ...
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3 votes
2 answers
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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/ ...
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3 votes
1 answer
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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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Align the HIV-1 Gag protein with the Gag protein of Visna virus

Align the HIV-1 Gag protein with the Gag protein of Visna virus Background Visna virus is a lentivirus causing encephalitis in sheep The problem is align the follow two protein Gag of viruses HIV-1 (...
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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 ...
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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 ...
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2 votes
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What is the typical host-to-bug DNA ratio found in nanopore sequencing without amplification?

I'm interested in sequencing human sputum sample (typically used for TB and SARS-CoV-2 using an ONT MinION without performing any type of whole genome DNA amplification or targeted PCR. Has anyone ...
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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' ...
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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 ...
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1 answer
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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 ...
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2 answers
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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 ...
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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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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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3 votes
1 answer
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RNA-seq analysis of mixed viral/host reads with salmon

I did RNA-seq of mammalian cells infected with pox virus. Now, I have read files which contain both host and virus reads. I want to align the reads both to host and viral genome. I was thinking I ...
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Annotation with Prokka or RAST

I was experimenting Prokka and RAST annotation tools. So, I took a well-annotated swinepox virus genome from genebank (NCBI Reference Sequence: NC_003389.1). I ran those sequences on Prokka and RAST ...
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1 vote
1 answer
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Using sickle for quality trimming

I am using sickle package from bioconda to trim my reads from the Illumina Miseq. When I tried following code, it failed to run ...
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How to create a SAF file for virus sequence?

I am trying to create a SAF file for the virus sequence. I can download .gff3 and .gb format for the virus gene sequence but they are not supported by featureCounts. I need to create my own SAF. I ...
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2 votes
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Label protein strucuture residues in Chimera

I have generated proteins structure of capsid protein of two strains of viruses. I have modeled them showing Coulombic electrostatic potential described below where positive charge is blue and ...
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3 votes
1 answer
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How to create a nexus file for BEAST?

I am learning to use BEAUTI and BEAST software. I followed their tutorial and was able to run example data without any problem. Now, I want to do phylodynamic analysis on my data. I have downloaded 70 ...
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Viral Load and Antiretroviral Therapy Dataset

My project is on Mathematical Modeling of the relationship between viral load and antiretroviral therapy. Its purely an academic investigation which is exploratory in nature. Question I am seeking a ...
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