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Related Concept Videos

Viruses with RNA Genomes01:29

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...
Human Virome01:26

Human Virome

The human body harbors a vast and diverse viral community known as the human virome. The virome includes bacteriophages that infect bacteria, and eukaryotic viruses that infect human cells. Transient dietary and environmental viruses also contribute to this dynamic ecosystem. Estimates suggest the human body may contain on the order of 10¹³ viral particles, though abundance varies widely by body site and detection method.Comprehensive characterization of the virome has become possible only with...
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 of Archaea

Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...
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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 for adaptive...
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Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.

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

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Published on: June 11, 2015

VIGOR extended to annotate genomes for additional 12 different viruses.

Shiliang Wang1, Jaideep P Sundaram, Timothy B Stockwell

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

Nucleic Acids Research
|June 7, 2012
PubMed
Summary

VIGOR is a gene prediction program that identifies viral genes and features using sequence similarity. It accurately detects complex genetic elements in 12 virus families, aiding in genomic analysis.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Virology

Background:

  • Gene prediction is crucial for understanding viral genomes.
  • Existing methods may not capture complex genetic features in diverse viral families.

Purpose of the Study:

  • To introduce VIGOR (Viral Genome ORF Reader), a gene prediction program.
  • To evaluate VIGOR's accuracy in identifying viral genes and complex features across multiple virus families.

Main Methods:

  • VIGOR utilizes sequence similarity searches against custom protein databases.
  • It identifies protein-coding regions, start/stop codons, RNA editing, and other gene features.
  • The program was tested on 27-240 viral genomes from GenBank for 12 virus families.

Main Results:

  • VIGOR successfully performs gene calling for various viruses, including coronaviruses, influenza, and 12 extended virus families.
  • Accurate identification of complex features such as RNA editing, stop codon leakage, and ribosomal shunting.
  • VIGOR's gene feature table facilitates GenBank submissions.

Conclusions:

  • VIGOR is an effective tool for viral gene prediction, handling complex genetic elements.
  • Its application aids in the genomic analysis and annotation of diverse viral sequences.
  • VIGOR supports infectious disease research by improving viral genome characterization.