The International Committee for Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Although taxonomy has often been based on virus phenotypic properties, such as capsid morphology, host range and disease associations, gene sequences and other genomic features provide a guide to their evolutionary relationships and may also be used in virus taxonomy.
GRAViTy - "Genome Relationships Applied to Virus Taxonomy" is an analysis pipeline that is effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into Orders (Aiewsakun and Simmonds, 2018). It can additionally be used to correctly differentiate assigned viruses from unassigned viruses and classify them into correct taxonomic groups. The method provides a rapid and objective means to explore metagenomic viral diversity and make informed recommendations for classification that are consistent with the current ICTV taxonomic framework. Methods like GRAViTy are increasingly required as the vast diversity of viruses found in metagenomic sequence datasets is explored.
The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification
Pakorn Aiewsakun, and Peter Simmonds
Microbiome 2018 6:38
Virus classification – where do you draw the line?
Peter Simmonds, and Pakorn Aiewsakun
Arch Virol. 2018; 163(8): 2037–2046
Evaluation of the genomic diversity of viruses infecting bacteria, archaea and eukaryotes using a common bioinformatic platform: steps towar
ds a unified taxonomy
Pakorn Aiewsakun, Evelien M. Adriaenssens, Rob Lavigne, Andrew M. Kropinski, and Peter Simmonds
J Gen Virol. 2018 Sep; 99(9): 1331–1343
A user guide containing information on how GRAViTy works, how to interpret the GRAViTy outputs, and information on running GRAViTy standalone is available here: GRAViTY_1.1_User_Guide.pdf
The algorithms within GRAViTy require coding complete genome sequences for taxonomic assignments. Submission of partial genome sequences will produce unreliable results that cannot be used for classification purposes.
GRAViTY jobs can take 6-12 hours to complete, and there is also a queue system for jobs running, so please be patient.
GRAViTy Job Messages & Errors
Upon clicking the 'Submit GRAViTy Job' button above, any errors associated with your submission will be shown here.
Example Input FASTA Sequence format
An example input is given here consisting of 4 viral genome sequences, with the third viral sequence consisting of multiple segments:
The below is a simple toy example to demonstrate how to structure segmented data - please do not copy and paste the below sequences and submit a GRAViTy job with them - it will not work as they a too short and not viral
The GRAViTy web server is housed at the MRC-University of Glasgow Centre for Virus Research, within the CVR Bioinformatics group. Please email Richard.Orton@glasgow.ac.uk for any issues with the server.