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VGO specifications


Unique identifier OMICS_15404
Name VGO
Alternative name Viral Genome Organizer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained No


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VGO citations


Genomic characterization of two novel pathogenic avipoxviruses isolated from pacific shearwaters (Ardenna spp.)

BMC Genomics
PMCID: 5390406
PMID: 28407753
DOI: 10.1186/s12864-017-3680-z

[…] ca) [], and the further analyses were conducted using the following tools: Viral Orthologous Clusters Database for sequence management (VOCs) []; Base-By-Base for genome/gene/protein alignments [, ]; Viral Genome Organizer for genome organization comparisons (VGO) [], and Genome Annotation Transfer Utility for annotation (GATU) [].Open reading frames (ORFs) longer than 60 amino acids with minimal […]


The UCSC Ebola Genome Portal

PLoS Curr
PMCID: 4318873
PMID: 25685613
DOI: 10.1371/currents.outbreaks.386ab0964ab4d6c8cb550bfb6071d822

[…] s collected epitope sequences from previously published studies. These diverse datasets can all be mapped to the genome sequence. However, existing tools such as the NCBI Virus Genome Browser and the Viral Genome Organizer show only gene models. VIPR is a toolset to annotate sequences but the results are not available instantly and does not merge them into an integrated zoomable view. Reasoning th […]


Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157

Microb Inform Exp
PMCID: 3372294
PMID: 22587704
DOI: 10.1186/2042-5783-1-12
call_split See protocol

[…] alignments (MSA) of protein sequences were generated using MUSCLE [], which has been incorporated into the Base-By-Base MSA editor []. Complete poxvirus genomes were visualized and analysed using the Viral Genome Organizer (VGO; []) tool at the Viral Bioinformatics Resource Centre (VBRC []).Prediction of the secondary structure of CRV-ZWE-157 and other DRBPs was performed with the Jpred secondary […]


JaPaFi: A Novel Program for the Identification of Highly Conserved DNA Sequences

PMCID: 3185747
PMID: 21994712
DOI: 10.3390/v2091867

[…] matches.Hit counts were determined by visualizing the output of the program for each parameter combination against a genome map of the Myxoma virus genome, which served as our model genome, using the Viral Genome Organizer software. The numbers of hits for each parameter combination were recorded in a hit-count matrix ().We chose a set of 11 hits for further examination based upon their consistent […]


The Genomic Diversity and Phylogenetic Relationship in the Family Iridoviridae

PMCID: 3185713
PMID: 21994690
DOI: 10.3390/v2071458
call_split See protocol

[…] ome sequences were obtained from the VOC database. Orthologous genes identified by the VOC software were confirmed by a BLAST search.G/C content analysis: G/C content analysis was completed using the Viral Genome Organizer (VGO) software [,]. The sequence for each genome was obtained from the VGO database. The software identified the G/C content of coding regions and this data was used to determin […]


Sequence Searcher: A Java tool to perform regular expression and fuzzy searches of multiple DNA and protein sequences

BMC Res Notes
PMCID: 2637886
PMID: 19183477
DOI: 10.1186/1756-0500-2-14

[…] patterns. Results are displayed in sortable tables and graphics are used to show fuzzy matches. To enable viewing of results with genome annotations, the core of SeqS has been incorporated in to the Viral Genome Organizer [] and Base-By-Base [] tools that can read GenBank files. […]


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