PHACTS, a computational approach to classifying the lifestyle of phages

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...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2012-03, Vol.28 (5), p.614-618
Main Authors: MCNAIR, Katelyn, BAILEY, Barbara A, EDWARDS, Robert A
Format: Article
Language:English
Subjects:
Algorithms
Bacteria - virology
Bacteriophages - genetics
Bacteriophages - physiology
BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology
Biological and medical sciences
Biotechnology & Applied Microbiology
Computer Science
Fundamental and applied biological sciences. Psychology
General aspects
Genomics - methods
Mathematical & Computational Biology
Mathematics
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Original Papers
Programming Languages
Software
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Summary: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. 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. 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 data are available at Bioinformatics online.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/bts014