Classifying the Unclassified: A Phage Classification Method

• Published in: Viruses Vol. 11; no. 2; p. 195
• Main Authors: Chibani, Cynthia Maria, Farr, Anton, Klama, Sandra, Dietrich, Sascha, Liesegang, Heiko
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 24.02.2019; MDPI
• Subjects: Bacteriophage Typing; Bacteriophages - classification; Bioinformatics; Cholera; Classification; Clustering; Conserved sequence; Datasets; Genome, Viral; Genomes; Genomics; Hidden Markov Models; Inoviridae; Lysogeny; Markov Chains; Metagenome; Myoviridae; New families; Nucleotide sequence; Phages; Phylogenetics; Phylogeny; Podoviridae; Podoviridae - classification; Prophages; Prophages - classification; protein coding sequences; Proteins; Siphoviridae; Siphoviridae - classification; Taxonomy; Vibrionaceae; vibriophages; Virulence; Virus Integration; Viruses; protein coding sequences; Keywords; Podoviridae; Siphoviridae; Vibrionaceae; phages; Hidden Markov Models; Inoviridae; classification; Myoviridae; vibriophages

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...