GRAViTy-V2

GRAViTy-V2 classifies viruses into taxonomic ranks through whole-genome analytical classification based on genomic sequence analysis.

Key Features:

• Expanded Feature Range: The tool encompasses a greatly expanded range of features and numerous optimisations compared to its predecessor framework.
• General-Purpose Classification: GRAViTy-V2 functions as a general-purpose virus classification tool applicable across diverse viral datasets.
• Multi-Level Taxonomic Resolution: The tool produces taxonomies equivalent to manually-curated versions down to the family level and in almost all cases to genus and species levels.
• ICTV Validation: GRAViTy-V2 was validated using 28 datasets derived from the ICTV 2022 taxonomy proposals and compared against human expert-curated classifications used for assignments in the 2023 round of ICTV taxonomy changes.
• Performance Benchmarking: Analysis times ranged from 1-506 min (median 3.59) on datasets with 17-1004 genomes and mean genome length of 3000-1 000 000 bases.

Scientific Applications:

• Viral Taxonomy Assignment: GRAViTy-V2 assigns viruses to taxonomic ranks including order, phylum, family, genus, and species.
• Higher-Rank Classification: Classification at higher taxonomic ranks such as order or phylum is based on alignment and comparison of amino acid sequence motifs in conserved genes.
• Lower-Rank Classification: Classification at lower taxonomic ranks such as genus or species is based on nucleotide sequence identities between genomic sequences.
• Taxonomy Proposal Evaluation: The tool supports evaluation of taxonomy proposals by comparison against expert-curated classifications for formal virus taxonomy processes.
• Annotation Quality Assessment: GRAViTy-V2 identifies discrepancies arising from errors in coding sequence annotations in INSDC records or from inclusion of incomplete genome sequences.

Methodology:

GRAViTy-V2 uses whole-genome analytical classification. For higher taxonomic ranks, it performs alignment and comparison of amino acid sequence motifs in conserved genes. For lower taxonomic ranks, it computes nucleotide sequence identities between genomic sequences. The tool was validated by comparing its output against human expert-curated classifications from ICTV 2022 taxonomy proposals.