2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2020

Cynthia Maria Chibani, Anton Farr, Sandra Klama, Sascha Dietrich, Heiko Liesegang. Classifying the Unclassified: A Phage Classification Method. Viruses, 11(2). 2019.

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Download from publisher: https://doi.org/10.3390/v11020195 PubMed

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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.