VirClust—A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of (Prokaryotic) Viruses

Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of viruses”, recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are c...

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Bibliographic Details
Published in:Viruses Vol. 15; no. 4; p. 1007
Main Author: Moraru, Cristina
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 19.04.2023
MDPI
Subjects:
bacteriophages
Bacteriophages - genetics
Classification
Cluster Analysis
Core protein
data collection
Genes
Genes, Viral
Genome, Viral
Genomes
Identification and classification
Markov chains
phage classification
Phylogenetics
Phylogeny
Physiological aspects
protein content
Proteins
Taxonomy
viral genome
Viral proteins
VirClust
virus classification
virus genome clustering
virus protein annotation
virus protein clustering
Viruses
Viruses - genetics
Germany
United States > US
VirClust
shared viral proteins
core proteins
phage classification
virus classification
virus protein clustering
virus genome clustering
virus protein annotation
ISSN:1999-4915, 1999-4915
Online Access:Get full text
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Summary:Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of viruses”, recognizes six different viral realms, defined based on the presence of viral hallmark genes (VHGs). Within the realms, viruses are classified into hierarchical taxons, ideally defined by the phylogeny of their shared genes. To enable the detection of shared genes, viruses have first to be clustered, and there is currently a need for tools to assist with virus clustering and classification. Here, VirClust is presented. It is a novel, reference-free tool capable of performing: (i) protein clustering, based on BLASTp and Hidden Markov Models (HMMs) similarities; (ii) hierarchical clustering of viruses based on intergenomic distances calculated from their shared protein content; (iii) identification of core proteins and (iv) annotation of viral proteins. VirClust has flexible parameters both for protein clustering and for splitting the viral genome tree into smaller genome clusters, corresponding to different taxonomic levels. Benchmarking on a phage dataset showed that the genome trees produced by VirClust match the current ICTV classification at family, sub-family and genus levels. VirClust is freely available, as a web-service and stand-alone tool.
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ISSN:1999-4915
1999-4915
DOI:10.3390/v15041007