VIGOR

VIGOR (Viral Genome ORF Reader) is a software tool to predict protein-coding sequences encoded by viruses. The VIGOR4 algorithm uses sequence similarity in curated VIGOR_DB (see data link below) for predictions and can detect frameshifts embedded and overlapping genes. In addition, the VIGOR4 includes algorithms to genotype influenza and rotavirus. The VIGOR_DB contains viral sequences for
Human Influenza A, B, C
Swine A, B, Avian A, B
Chikungunya Virus, Eastern Equine Encephalitis Virus
Respiratory Syncytial Virus
SARS-CoV-2, Enterovirus
Lassa Mammarenavirus, West Nile Virus
Zika Virus, Rotavirus
Influenza A/B/C Virus, Lassa Mammarenavirus
Respiratory Syncytial Virus
Rotavirus A/B/C/F/G, Sapovirus
SARSCoV2, Alphaviruses
West Nile Virus Lineage I/II, Zika Virus
Hantaviridae, Nairoviridae
Peribunyaviridae, Sarbecovirus
Nobecovirus, Hibecovirus
Embecovirus, Merbecovirus
Monkeypox Virus, Beidivirus
Coguvirus, Dengue virus
Entovirus, Goukovirus
Horwuvirus, Hudivirus
Hudovirus, Ixovirus
Laulavirus, Lentinuvirus
Mobuvirus, Phasivirus
Phlebovirus, Merbecovirus
Monkeypox Virus, Beidivirus
Coguvirus, Dengue virus
Entovirus, Goukovirus
Horwuvirus, Hudivirus
Hudovirus, Ixovirus
Laulavirus, Lentinuvirus
Mobuvirus. Phasivirus
Phlebovirus

Topic

Gene transcripts;Gene structure;Gene expression

Detail

  • Operation: Homology-based gene prediction;Gene prediction;Coding region prediction;Protein feature detection

  • Software interface: Web user interface

  • Language: Java

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 3 and 4

  • Credit: The Genomic Sequencing Centers for Infectious Diseases (GSCID), the Genomic Centers for Infectious Diseases (GCID), and the Bioinformatics Resource Centers (BRC), part of National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH).

  • Input: -

  • Output: -

  • Contact: jps228@georgetown.edu, isingh@jcvi.org

  • Collection: -

  • Maturity: Mature

Publications

  • VIGOR extended to annotate genomes for additional 12 different viruses.
  • Wang S, Sundaram JP, Stockwell TB. VIGOR extended to annotate genomes for additional 12 different viruses. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W186-92. doi: 10.1093/nar/gks528. Epub 2012 Jun 4. PMID: 22669909; PMCID: PMC3394299.
  • https://doi.org/10.1093/nar/gks528
  • PMID: 22669909
  • PMC: PMC3394299
  • VIGOR: Interactive Visual Exploration of Graph Query Results.
  • Pienta R, Hohman F, Endert A, Tamersoy A, Roundy K, Gates C, Navathe S, Chau DH. VIGOR: Interactive Visual Exploration of Graph Query Results. IEEE Trans Vis Comput Graph. 2018 Jan;24(1):215-225. doi: 10.1109/TVCG.2017.2744898. Epub 2017 Aug 29. PMID: 28866563.
  • https://doi.org/10.1109/TVCG.2017.2744898
  • PMID: 28866563
  • PMC: -
  • VIGOR, an annotation program for small viral genomes
  • Wang S, Sundaram JP, Spiro D. VIGOR, an annotation program for small viral genomes. BMC Bioinformatics. 2010 Sep 7;11:451. doi: 10.1186/1471-2105-11-451. PMID: 20822531; PMCID: PMC2942859.
  • https://doi.org/10.1186/1471-2105-11-451
  • PMID: 20822531
  • PMC: PMC2942859

Download and documentation

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