PHAST: A Fast Phage Search Tool

By You Zhou, Yongjie Liang, Karlene H. Lynch, J. Dennis, David S. Wishart. Nucleic Acids Res., 2011

1,981 citations recorded by the source corpus.

PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage ‘cornerstone’ feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage ‘quality’ and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at (http://phast.wishartlab.com).

Subfields: Ecology, Microbiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bd11843aa20db8942e69e9fe2ba5343370c5cc96

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

1. Jed A. Fuhrman
2. David S. Wishart
3. Fengzhu Sun
4. S. Abedon
5. Yang Young Lu
6. Matthew B. Sullivan
7. Nathan A. Ahlgren
8. Jie Jessie Ren

In Microbiology

1. David S. Wishart
2. S. Abedon
3. Matthew B. Sullivan

In Molecular Biology

1. David S. Wishart
2. Allison Pon
3. David Arndt
4. Jed A. Fuhrman
5. Fengzhu Sun
6. Jason R. Grant
7. Yang Young Lu
8. Matthew B. Sullivan

Citations in the corpus

• Lysogeny in nature: mechanisms, impact and ecology of temperate phages (2017, background): “Prophage sequences can be identified from whole or draft microbial isolate genomes (Lima-Mendez et al., 2008; Zhou et al., 2011; Akhter et al., 2012; Roux et al., 2015a); theoretically from single-cell genomes (Roux et al.”
• PHASTER: a better, faster version of the PHAST phage search tool (2016, background): “First published in 2011 (2), PHAST has become one of the most popular tools for prophage identification in bacterial genomes.”
• VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data (2017, methodology): “Additionally, most of these prophage predictors are not optimized to process large numbers of contigs in a reasonable time (see [13]), the exception being PHASTER, an updated version of PHAST [14].”