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Classifying the Unclassified: A Phage Classification Method

This work reports the method ClassiPhage to classify phage genomes using sequence derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov Models (HMMs) generated from clusters of related proteins. The method was validated on all publicly available genomes of phages that ar...

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Autores principales: Chibani, Cynthia Maria, Farr, Anton, Klama, Sandra, Dietrich, Sascha, Liesegang, Heiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409715/
https://www.ncbi.nlm.nih.gov/pubmed/30813498
http://dx.doi.org/10.3390/v11020195
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author Chibani, Cynthia Maria
Farr, Anton
Klama, Sandra
Dietrich, Sascha
Liesegang, Heiko
author_facet Chibani, Cynthia Maria
Farr, Anton
Klama, Sandra
Dietrich, Sascha
Liesegang, Heiko
author_sort Chibani, Cynthia Maria
collection PubMed
description This work reports the method ClassiPhage to classify phage genomes using sequence derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov Models (HMMs) generated from clusters of related proteins. The method was validated on all publicly available genomes of phages that are known to infect Vibrionaceae. The phages belong to the well-described phage families of Myoviridae, Podoviridae, Siphoviridae, and Inoviridae. The achieved classification is consistent with the assignments of the International Committee on Taxonomy of Viruses (ICTV), all tested phages were assigned to the corresponding group of the ICTV-database. In addition, 44 out of 58 genomes of Vibrio phages not yet classified could be assigned to a phage family. The remaining 14 genomes may represent phages of new families or subfamilies. Comparative genomics indicates that the ability of the approach to identify and classify phages is correlated to the conserved genomic organization. ClassiPhage classifies phages exclusively based on genome sequence data and can be applied on distinct phage genomes as well as on prophage regions within host genomes. Possible applications include (a) classifying phages from assembled metagenomes; and (b) the identification and classification of integrated prophages and the splitting of phage families into subfamilies.
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spelling pubmed-64097152019-04-01 Classifying the Unclassified: A Phage Classification Method Chibani, Cynthia Maria Farr, Anton Klama, Sandra Dietrich, Sascha Liesegang, Heiko Viruses Article This work reports the method ClassiPhage to classify phage genomes using sequence derived taxonomic features. ClassiPhage uses a set of phage specific Hidden Markov Models (HMMs) generated from clusters of related proteins. The method was validated on all publicly available genomes of phages that are known to infect Vibrionaceae. The phages belong to the well-described phage families of Myoviridae, Podoviridae, Siphoviridae, and Inoviridae. The achieved classification is consistent with the assignments of the International Committee on Taxonomy of Viruses (ICTV), all tested phages were assigned to the corresponding group of the ICTV-database. In addition, 44 out of 58 genomes of Vibrio phages not yet classified could be assigned to a phage family. The remaining 14 genomes may represent phages of new families or subfamilies. Comparative genomics indicates that the ability of the approach to identify and classify phages is correlated to the conserved genomic organization. ClassiPhage classifies phages exclusively based on genome sequence data and can be applied on distinct phage genomes as well as on prophage regions within host genomes. Possible applications include (a) classifying phages from assembled metagenomes; and (b) the identification and classification of integrated prophages and the splitting of phage families into subfamilies. MDPI 2019-02-24 /pmc/articles/PMC6409715/ /pubmed/30813498 http://dx.doi.org/10.3390/v11020195 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Chibani, Cynthia Maria
Farr, Anton
Klama, Sandra
Dietrich, Sascha
Liesegang, Heiko
Classifying the Unclassified: A Phage Classification Method
title Classifying the Unclassified: A Phage Classification Method
title_full Classifying the Unclassified: A Phage Classification Method
title_fullStr Classifying the Unclassified: A Phage Classification Method
title_full_unstemmed Classifying the Unclassified: A Phage Classification Method
title_short Classifying the Unclassified: A Phage Classification Method
title_sort classifying the unclassified: a phage classification method
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6409715/
https://www.ncbi.nlm.nih.gov/pubmed/30813498
http://dx.doi.org/10.3390/v11020195
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