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VIGOR specifications

Information


Unique identifier OMICS_17585
Name VIGOR
Alternative name Viral Genome ORF Reader
Interface Web user interface
Restrictions to use None
Input format FASTA
Programming languages Perl, PHP
Computer skills Basic
Stability Stable
Maintained No

Documentation


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Publication for Viral Genome ORF Reader

VIGOR citations

 (12)
library_books

Genomic analysis of a large set of currently—and historically—important human adenovirus pathogens

2018
PMCID: 5837155
PMID: 29410402
DOI: 10.1038/s41426-017-0004-y

[…] The sequences were annotated with a viral annotation software, Viral Genome ORF Reader (VIGOR), prior to GenBank submission. To identify and to query for novel penton base, hexon, and fiber genes, BLAST was used as well as a genotyping software tool for the hexon […]

call_split

Genome Sequence of Enterovirus D68 from Saint Louis, Missouri, USA, 2016

2017
Genome Announc
PMCID: 5334578
PMID: 28254971
DOI: 10.1128/genomeA.01630-16
call_split See protocol

[…] ligned back to the assembly using BWA mem (), and contigs and aligned sequence reads were visualized using Tablet (). Contig sequences were manually reviewed and improved. Genomes were annotated with VIGOR (, ).The two St. Louis viruses showed greater than 99% nucleic acid and predicted amino acid sequence identity to each other and to other 2016 strains that had been deposited into GenBank as of […]

call_split

Respiratory Syncytial Virus whole genome sequencing identifies convergent evolution of sequence duplication in the C terminus of the G gene

2016
Sci Rep
PMCID: 4876326
PMID: 27212633
DOI: 10.1038/srep26311
call_split See protocol

[…] tion sequences to the updated reference sequences was performed with CLC Bio’s clc_ref_assemble_long program. Curated assemblies were validated and annotated with the viral annotation software called Viral Genome ORF Reader, VIGOR 3.0, before submission to GenBank. VIGOR was used to predict genes, perform alignments, ensure the fidelity of open reading frames, correlate nucleotide polymorphisms wi […]

library_books

Isolation and Characterization of a Novel Gammaherpesvirus from a Microbat Cell Line

2016
PMCID: 4863610
PMID: 27303702
DOI: 10.1128/mSphere.00070-15

[…] e used to join the contigs generated from the HiSeq data into a single sequence of 129,563 bases (). To annotate the assembled BGHV8, we developed gammaherpesvirus-specific annotation software in the Viral Genome ORF Reader (VIGOR) software () with relaxed parameters on the percent similarity cutoff, to accommodate the variation in herpesvirus genomes. VIGOR was used to predict genes, perform alig […]

call_split

First Complete Genome Sequences of Two Keystone Viruses from Florida

2015
Genome Announc
PMCID: 4626608
PMID: 26514762
DOI: 10.1128/genomeA.01255-15
call_split See protocol

[…] segments shared an 11-bp conserved 5′ terminal sequence, in coding sense (5′-AGTAGTGTACT-3′) and a 3′ terminal sequence, in coding sense (5′-GAGCACACTAC-3′). The final assemblies were annotated using VIGOR (, ) and submitted to GenBank.Comparing these two KEYV genomes with other CAL serogroup virus genomes shows a high degree of sequence diversity; the S, M, and L segments show nucleotide similari […]

call_split

Genetic Characterization of the Belgian Nephropathogenic Infectious Bronchitis Virus (NIBV) Reference Strain B1648

2015
Viruses
PMCID: 4576188
PMID: 26262637
DOI: 10.3390/v7082827
call_split See protocol

[…] lug-in in the MEGA software version 5.2.2, followed by manual editing. The B1648 genome, coding sequence and ORF prediction was carried out in http://covdb.microbiology.hku.hk and http://www.jcvi.org/vigor/ [,]. Phylogenetic trees were constructed using the maximum-likelihood method. Substitution models were determined for each gene separately. The bootstrap values were determined from 500 replica […]

Citations

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VIGOR institution(s)
J. Craig Venter Institute, Medical Center Drive, Rockville, MD, USA; Computational Genomics Laboratory, Department of Biology, Georgetown University Georgetown, Washington DC, WA, USA
VIGOR funding source(s)
Supported by National Institute of Allergy contracts N01-AI-30071 and HHSN272200900007C.

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