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

• Published in: Briefings in bioinformatics Vol. 20; no. 4; pp. 1560 - 1567
• Main Authors: Arndt, David, Marcu, Ana, Liang, Yongjie, Wishart, David S
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19.07.2019; Oxford Publishing Limited (England)
• Subjects: Bacteria; Computational Biology; Data Mining - trends; Databases, Genetic; Gene sequencing; Genome, Bacterial; Genomes; Internet; Internet resources; Metagenomics; Phages; Prophages; Prophages - genetics; Search Engine - trends; Servers; Software - trends; Software Review; User-Computer Interface; Whole genome sequencing; prophage; phage; bacterial genome; metagenomics; bioinformatics
• ISSN: 1467-5463; 1477-4054; 1477-4054
• DOI: 10.1093/bib/bbx121

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).