VGO

VGO organizes and visualizes poxvirus genomes to support analysis, annotation, and comparative genomics of the Poxviridae family including variola virus and monkeypox virus.

Key Features:

• Genome Visualization: Provides a genome browser displaying genes, open reading frames (ORFs), and start/stop codons for viral genomes.
• Search Capabilities: Supports regular expression searches, fuzzy motif searches, and masslist searches for sequence pattern matching and large-scale sequence comparison.
• Comparative Genomics: Compares viral genomes against the Variants Of Concern (VOCs) genome sequence database to identify genetic variation.
• Data Integration and Annotation: Integrates over 35 complete genomic sequences from multiple Poxviridae genera, species, and strains and annotates sequences using GenBank and unpublished sequence data.
• Analytical Tools: Includes tools for comparative analysis of different virus isolates to discern functional and evolutionary differences.
• Visualization Tools: Offers advanced visualization capabilities for interpreting genomic and comparative analysis results.

Scientific Applications:

• Poxvirus genomic characterization: Supports analysis of Poxviridae genomes, including variola virus and monkeypox virus.
• Surveillance and variant detection: Facilitates detection and comparison of variants using the Variants Of Concern (VOCs) genome sequence database.
• Marker identification: Aids identification of genetic markers associated with virulence, transmission, and vaccine development.
• Comparative evolutionary studies: Enables comparative genomics to study evolutionary relationships among virus isolates.

Methodology:

Implements a genome browser for gene/ORF/start–stop visualization; supports regular expression, fuzzy motif, and masslist searches; performs comparative genomics against the Variants Of Concern (VOCs) genome sequence database; and integrates and annotates over 35 Poxviridae genomes from GenBank and unpublished sequences for downstream comparative analyses.