Next Article in Journal
Duck Plague Virus Promotes DEF Cell Apoptosis by Activating Caspases, Increasing Intracellular ROS Levels and Inducing Cell Cycle S-Phase Arrest
Next Article in Special Issue
Prevalence and Diversity Analysis of Candidate Prophages to Provide An Understanding on Their Roles in Bacillus Thuringiensis
Previous Article in Journal
Priorities, Barriers, and Facilitators towards International Guidelines for the Delivery of Supportive Clinical Care during an Ebola Outbreak: A Cross-Sectional Survey
Previous Article in Special Issue
Host Resistance, Genomics and Population Dynamics in a Salmonella Enteritidis and Phage System
Article Menu
Issue 2 (February) cover image

Export Article

Open AccessArticle

Classifying the Unclassified: A Phage Classification Method

Institute for Microbiology and Genetics, Georg-August University Goettingen, Grisebachstr. 8, 37077 Goettingen, Germany
Author to whom correspondence should be addressed.
Viruses 2019, 11(2), 195;
Received: 21 December 2018 / Revised: 6 February 2019 / Accepted: 20 February 2019 / Published: 24 February 2019
(This article belongs to the Special Issue Diversity and Evolution of Phage Genomes)
PDF [1893 KB, uploaded 27 February 2019]
  |     |  


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. View Full-Text
Keywords: Hidden Markov Models; Vibrionaceae; vibriophages; Inoviridae; Myoviridae; Podoviridae; Siphoviridae; phages; classification; protein coding sequences Hidden Markov Models; Vibrionaceae; vibriophages; Inoviridae; Myoviridae; Podoviridae; Siphoviridae; phages; classification; protein coding sequences

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material


Share & Cite This Article

MDPI and ACS Style

Chibani, C.M.; Farr, A.; Klama, S.; Dietrich, S.; Liesegang, H. Classifying the Unclassified: A Phage Classification Method. Viruses 2019, 11, 195.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics



[Return to top]
Viruses EISSN 1999-4915 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top