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Review
. 2019 Jul 19;20(4):1560-1567.
doi: 10.1093/bib/bbx121.

PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes

David Arndt, Ana Marcu, Yongjie Liang, David S Wishart
Review

PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes

David Arndt et al. Brief Bioinform. .

Abstract

PHAST (PHAge Search Tool) and its successor PHASTER (PHAge Search Tool - Enhanced Release) have become two of the most widely used web servers for identifying putative prophages in bacterial genomes. Here we review the main capabilities of these web resources, provide some practical guidance regarding their use and discuss possible future improvements. PHAST, which was first described in 2011, made its debut just as whole bacterial genome sequencing and was becoming inexpensive and relatively routine. PHAST quickly gained popularity among bacterial genome researchers because of its web accessibility, its ease of use along with its enhanced accuracy and rapid processing times. PHASTER, which appeared in 2016, provided a number of much-needed enhancements to the PHAST server, including greater processing speed (to cope with very large submission volumes), increased database sizes, a more modern user interface, improved graphical displays and support for metagenomic submissions. Continuing developments in the field, along with increased interest in automated phage and prophage finding, have already led to several improvements to the PHASTER server and will soon lead to the development of a successor to PHASTER (to be called PHASTEST).

Keywords: bacterial genome; bioinformatics; metagenomics; phage; prophage.

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Figures

Figure 1
Figure 1
A montage of PHAST output images. A colour version of this figure is available at BIB online: https://academic.oup.com/bib.
Figure 2
Figure 2
A screenshot of PHASTER’s modernized user interface. A colour version of this figure is available at BIB online: https://academic.oup.com/bib.
See this image and copyright information in PMC

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