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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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
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Abstract	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.
AbstractList	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. 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.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.
Audience	Academic
Author	Moraru, Cristina
AuthorAffiliation	Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky–Str. 9-11, 26111 Oldenburg, Germany; liliana.cristina.moraru@uni-oldenburg.de
AuthorAffiliation_xml	– name: Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky–Str. 9-11, 26111 Oldenburg, Germany; liliana.cristina.moraru@uni-oldenburg.de
Author_xml	– sequence: 1 givenname: Cristina orcidid: 0000-0002-5375-5437 surname: Moraru fullname: Moraru, Cristina
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Snippet	Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called “megataxonomy of... Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current classification scheme, also called "megataxonomy of...
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SubjectTerms	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
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Title	VirClust—A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of (Prokaryotic) Viruses
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