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Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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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...
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Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
08:31

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

Published on: May 26, 2013

VIGOR, an annotation program for small viral genomes.

Shiliang Wang1, Jaideep P Sundaram, David Spiro

  • 1J, Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA. shiliang@jcvi.org

BMC Bioinformatics
|September 9, 2010
PubMed
Summary
This summary is machine-generated.

VIGOR is a new web tool for accurate gene prediction in RNA viruses like influenza and rotavirus. This tool aids in rapid genome annotation and surveillance of infectious diseases.

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Related Experiment Videos

Last Updated: Jun 9, 2026

Isolation and Genome Analysis of Single Virions using 'Single Virus Genomics'
08:31

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

Published on: May 26, 2013

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

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Published on: June 11, 2015

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10:18

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Virology

Background:

  • Decreasing sequencing costs and improving technologies facilitate rapid genome sequencing, particularly for microbial and viral pathogens.
  • Accurate gene prediction remains a challenge for newly sequenced genomes, hindering efficient analysis.
  • There is a need for effective gene prediction tools for rapid surveillance of RNA viruses via full genome sequencing.

Purpose of the Study:

  • To develop a user-friendly, web-based tool for accurate gene prediction in various RNA viral genomes.
  • To provide a tool capable of identifying specific viral genome features and performing genotyping.

Main Methods:

  • Developed VIGOR (Viral Genome ORF Reader), a web application for gene prediction.
  • VIGOR utilizes sequence similarity searches to detect protein-coding regions.
  • The tool identifies genome-specific features like frame shifts, overlapping genes, and embedded genes.

Main Results:

  • VIGOR accurately predicts protein-coding genes in influenza, rotavirus, rhinovirus, and coronavirus subtypes with >99% specificity and sensitivity.
  • The tool can detect mature peptides within open reading frames and includes genotyping for influenza and rotavirus.
  • VIGOR outperforms existing gene prediction programs like ZCURVE_V, GeneMarkS, and FLAN.

Conclusions:

  • VIGOR is a user-friendly, web-based annotation program for five viral agents, offering public access for rotavirus and rhinovirus gene prediction.
  • It accurately predicts protein-coding genes, assigns function to ORFs, and genotypes influenza viruses.
  • VIGOR is designed for high-throughput annotation in post-sequencing pipelines, aiding in infectious disease surveillance.