PHASTER: a better, faster version of the PHAST phage search tool

Abstract

PHASTER (PHAge Search Tool – Enhanced Release) is a significant upgrade to the popular PHAST web server for the rapid identification and annotation of prophage sequences within bacterial genomes and plasmids. Although the steps in the phage identification pipeline in PHASTER remain largely the same as in the original PHAST, numerous software improvements and significant hardware enhancements have now made PHASTER faster, more efficient, more visually appealing and much more user friendly. In particular, PHASTER is now 4.3× faster than PHAST when analyzing a typical bacterial genome. More specifically, software optimizations have made the backend of PHASTER 2.7X faster than PHAST, while the addition of 80 CPUs to the PHASTER compute cluster are responsible for the remaining speed-up. PHASTER can now process a typical bacterial genome in 3 min from the raw sequence alone, or in 1.5 min when given a pre-annotated GenBank file. A number of other optimizations have also been implemented, including automated algorithms to reduce the size and redundancy of PHASTER's databases, improvements in handling multiple (metagenomic) queries and higher user traffic, along with the ability to perform automated look-ups against 14 000 previously PHAST/PHASTER annotated bacterial genomes (which can lead to complete phage annotations in seconds as opposed to minutes). PHASTER's web interface has also been entirely rewritten. A new graphical genome browser has been added, gene/genome visualization tools have been improved, and the graphical interface is now more modern, robust and user-friendly. PHASTER is available online at www.phaster.ca.

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

“…Both are described as pathogenic bacteria. We then identified important differences between them, by comparing the prophage sequences annotated using PHASTER (e < 10 −4 ) (Arndt et al, 2016). Two prophage regions were annotated in the genome of the human microbiome isolate.…”

Genome-Wide Analysis Provides Evidence on the Genetic Relatedness of the EmergentXylella fastidiosaGenotype in Italy to Isolates from Central America

“…pauca (henceforth referred to as "alignment reference genome") based on a BLAST+ analysis performed on a local computer, with default options and parameter values of 50% lower -70% upper cut-off for identity and E-value threshold of 10 _ 5 . The online software PHASTER (faster version of the PHAST phage search tool) (Arndt et al 2016) was used to identify DNA prophage regions in the chromosome drafts of the four available ST53 isolates.…”

Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study

“…Furthermore, the ResFinder 3.0 (https://cge.cbs.dtu.dk//services/ResFinder/) (Zankari et al, 2012) and PathogenFinder 1.1 (https://cge.cbs.dtu.dk/services/PathogenFinder/) (Cosentino et al, 2013) were used for identifying the acquired antibiotic resistance genes and pathogenicity factors, respectively. Clustered regularly interspersed short palindromic repeats (CRISPR) and prophage sequences were identified by CRISPR Finder (http://crispr.i2bc.paris-saclay.fr/Server/) (Grissa et al, 2007) and PHASTER (http://phaster.ca/) (Arndt et al, 2016), respectively. The predicted genes were annotated against the restriction enzyme database (REBASE, http://tools.neb.com/genomes/) (Roberts et al, 2015) for searching restriction enzyme.…”