Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Viruses with RNA Genomes

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...

Subviral Agents

Subviral Agents

Subviral agents are infectious entities that resemble viruses but lack one or more viral components, such as a capsid or essential replication machinery. These agents include viroids, prions, and satellites, each possessing distinct structural and functional characteristics that influence their mode of infection and replication.Viroids are the simplest subviral agents, consisting of circular, single-stranded RNA molecules without a protein coat. They exclusively infect plants, relying entirely...

Viral Recombination

Viral Recombination

Cells are sometimes infected by more than one virus at once. When two viruses disassemble to expose their genomes for replication in the same cell, similar regions of their genomes can pair together and exchange sequences in a process called recombination. Alternatively, viruses with segmented genomes can swap segments in a process called reassortment.

Viral Mutations

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...

Introduction to Virus

Introduction to Virus

Viruses are unique biological entities that blur the boundary between living and non-living systems. Although they lack cellular structure and metabolic processes, they can exhibit characteristics of life when infecting a host. Their defining feature is a nucleic acid core, composed of either DNA or RNA, encapsulated within a protein coat called a capsid. This simple structure allows them to invade host cells and use their machinery for replication efficiently.Viral Structure and...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Alignment-free detection of differences between sequencing datasets.

iScience·2025

Same author

Differential quantification of alternative splicing events on spliced pangenome graphs.

PLoS computational biology·2024

Same author

PangeBlocks: customized construction of pangenome graphs via maximal blocks.

BMC bioinformatics·2024

Same author

Diverse somatic Transformer and sex chromosome karyotype pathways regulate gene expression in Drosophila gonad development.

bioRxiv : the preprint server for biology·2024

Same author

Data Structures for SMEM-Finding in the PBWT.

International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)·2024

Same author

RecGraph: recombination-aware alignment of sequences to variation graphs.

Bioinformatics (Oxford, England)·2024

Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

Same journal

Dual channel drug-drug interactions extraction based on cross attention.

BMC bioinformatics·2026

Same journal

FeSseqdb: a curated sequence-level database and interpretable machine learning framework for identifying iron-sulfur proteins.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Sep 26, 2025

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

MALVIRUS: an integrated application for viral variant analysis.

Simone Ciccolella¹, Luca Denti^1,2, Paola Bonizzoni¹

¹Department of Informatics, Systems and Communication, University of Milano-Bicocca, Viale Sarca 336, 20136, Milan, Italy.

BMC Bioinformatics

|April 20, 2022

Summary

This summary is machine-generated.

MALVIRUS is a new application for analyzing viral populations, like SARS-CoV-2. It efficiently identifies variants and assigns lineages, improving viral strain tracking.

Keywords:

Genotyping Lineage classification SARS-CoV-2 Sequence analysis Virus

More Related Videos

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

Related Experiment Videos

Last Updated: Sep 26, 2025

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Amplification, Next-generation Sequencing, and Genomic DNA Mapping of Retroviral Integration Sites

Published on: March 22, 2016

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'

Published on: May 26, 2013

Area of Science:

Genomics
Bioinformatics
Virology

Background:

Efficiently calling variants from viral sequencing data is crucial for tracking global spread, as highlighted by the COVID-19 pandemic.
The increasing volume of daily sequencing data necessitates advanced analytical tools for viral population studies.

Purpose of the Study:

To present MALVIRUS, an accessible application designed for comprehensive viral population analysis.
To facilitate variant catalog construction, genotyping, annotation, and lineage assignment for viral samples, including SARS-CoV-2.

Main Methods:

MALVIRUS constructs a variant catalog of SNPs/indels from population sequences.
It efficiently genotypes and annotates catalog variants using read samples.
For SARS-CoV-2, it assigns samples to Pango lineages based on genotyped variations.

Main Results:

MALVIRUS demonstrated efficiency and effectiveness on both Illumina and Nanopore sequencing data for SARS-CoV-2 analysis.
Performance was validated against public NCBI and comprehensive GISAID datasets.
Comparative analysis showed MALVIRUS offers superior precision and recall compared to existing state-of-the-art tools.

Conclusions:

MALVIRUS is a highly effective tool for analyzing SARS-CoV-2 strains.
The application provides enhanced precision and recall in variant analysis.
Its ease of installation and use makes it valuable for viral population studies.