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. 2012 Mar 1;28(5):614-8.
doi: 10.1093/bioinformatics/bts014. Epub 2012 Jan 11.

PHACTS, a computational approach to classifying the lifestyle of phages

Katelyn McNair  1 , Barbara A Bailey, Robert A Edwards
Affiliations

PHACTS, a computational approach to classifying the lifestyle of phages

Katelyn McNair et al. Bioinformatics. .

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/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Accuracy of PHACTS predictions when classifying the lifestyle of the 227 phages with known lifestyles. A confident classification is where the averaged replicate predictions are >2 SD apart.
Fig. 2.
Fig. 2.
The correlation between the protein function and the importance toward lifestyle predictions. Phage functional modules are proteins that have functions that are unique to phages, such as capsid assembly or phage DNA packaging.
Fig. 3.
Fig. 3.
The effect of incomplete phage proteomes on the accuracy of PHACTS lifestyle predictions.
See this image and copyright information in PMC

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