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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Dec 6, 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

VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data.

Yoshiaki Yasumizu¹, Atsushi Hara², Shimon Sakaguchi¹

¹Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan.

Bioinformatics (Oxford, England)

|October 5, 2020

Summary

A new bioinformatics tool, VIRTUS, analyzes virus-transcribed messenger RNAs (mRNAs) in human cells. This tool detects hundreds of viruses, aiding in understanding covert viral infections and developing targeted treatments.

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Last Updated: Dec 6, 2025

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

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Published on: July 27, 2018

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Published on: June 30, 2023

Area of Science:

Bioinformatics
Virology
Genomics

Background:

Clinical samples may contain abundant viral RNA transcripts, a factor often overlooked.
Existing methods may not adequately distinguish viral from host RNA or quantify viral gene expression.

Purpose of the Study:

To develop a novel bioinformatics pipeline for analyzing virus-transcribed mRNAs.
To enable the detection and quantification of viral transcripts in bulk and single-cell RNA-sequencing data.
To facilitate the simultaneous assessment of viral infection, viral composition, and host gene expression.

Main Methods:

Development of VIRTUS (VIRal Transcript Usage Sensor) pipeline.
Utilizing Common Workflow Language and Docker for implementation.
Application to bulk and single-cell RNA-sequencing data of human cells.

Main Results:

VIRTUS successfully detected and quantified transcripts from 762 viruses, including herpesviruses, retroviruses, and SARS-CoV-2.
The tool enabled simultaneous identification of infected cells, multiple viral co-infections, and host gene expression profiles.
Demonstrated capability to analyze viral mRNA, not just viral copy numbers.

Conclusions:

VIRTUS is a powerful bioinformatics tool for studying viral infections through transcriptomic analysis.
This method can reveal the impact of latent viruses on diseases.
It offers a pathway for developing novel antiviral therapies targeting specific viruses.