PHACTS, a computational approach to classifying the lifestyle of phages

Abstract

Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed.Results: Phage Classification Tool Set (PHACTS) utilizes a novel similarity algorithm and a supervised Random Forest classifier to make a prediction whether the lifestyle of a phage, described by its proteome, is virulent or temperate. The similarity algorithm creates a training set from phages with known lifestyles and along with the lifestyle annotation, trains a Random Forest to classify the lifestyle of a phage. PHACTS predictions are shown to have a 99% precision rate.Availability and implementation: PHACTS was implemented in the PERL programming language and utilizes the FASTA program (Pearson and Lipman, 1988) and the R programming language library ‘Random Forest’ (Liaw and Weiner, 2010). The PHACTS software is open source and is available as downloadable stand-alone version or can be accessed online as a user-friendly web interface. The source code, help files and online version are available at http://www.phantome.org/PHACTS/.Contact: katelyn@rohan.sdsu.edu; redwards@sciences.sdsu.eduSupplementary information: Supplementary data are available at Bioinformatics online.

Characterization and complete genome sequence analysis of Staphylococcus aureus bacteriophage JS01

“…The complete JS01 genome sequence showed 75 % query cover and 99 % identity with Staphylococcus prophage PVL (GenBank Accession Number NC_002321.1), along with 85 % coverage and 99 % identity with S. aureus MSSA476 (BX571857.1). These results suggest that JS01 is a temperate phage, consistent with predictions from the Phage Classification Tool Set (PHACTS) [6]. The gene-coding potential of the global genome is 88.9 %.…”

Contributions of P2- and P22-like prophages to understanding the enormous diversity and abundance of tailed bacteriophages

“…Therefore, the presence or absence of closely related MCPs encoded by the genomes of the authentic phage’s host or closely related bacteria indicates that the phage is almost certainly temperate or lytic, respectively. This very simple test was as accurate or better at determining lifestyle than was reported for the computer program PHACTS, which uses a training set of phages with known lifestyles (McNair et al , 2012). In addition, it was as good at finding prophages (that have not degraded or deleted their MCP gene) as Prophinder and Phage_Finder, which detect phage-gene enriched regions and genomic context to identify prophages (Fouts, 2006; Lima-Mendez et al , 2008).…”

High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils

“…The presence of tRNAs in annotated contigs was assessed with the tRNAscanSE software accessible through http://lowelab.ucsc.edu/tRNAscan-SE/ (29). For prediction of phage lifestyle and host Gram stain reaction, whole-genome protein sequences of candidate phage genomes were submitted to the online version of PHACTS (http://www.phantome.org/PHACTS/) (30). Aligned marker genes showing sufficient homology (Ͼ150 bp; MetaVir) against the contigs were recovered, and phylogenetic analysis was performed using MEGA5 (http://www.megasoftware.net/).…”