| PHACTS, a computational approach to classifying the lifestyle of phages. | |
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MedLine Citation:
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PMID: 22238260 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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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: 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 [29] and the R programming language library "Random Forest" [30]. 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.edu* |
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Authors:
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Katelyn McNair; Barbara A Bailey; Robert A Edwards |
Publication Detail:
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Type: JOURNAL ARTICLE Date: 2012-1-11 |
Journal Detail:
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Title: Bioinformatics (Oxford, England) Volume: - ISSN: 1367-4811 ISO Abbreviation: - Publication Date: 2012 Jan |
Date Detail:
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Created Date: 2012-1-12 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9808944 Medline TA: Bioinformatics Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
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Computational Science Research Center, Department of Mathematics and Statistics, Department of Computer Science, San Diego State University, San Diego, California 92182, Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, Illinois 60439. |
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