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Related Experiment Video

Updated: Jun 1, 2026

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins
09:40

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

PHAST: a fast phage search tool.

You Zhou1, Yongjie Liang, Karlene H Lynch

  • 1Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada T6G 2E8.

Nucleic Acids Research
|June 16, 2011
PubMed
Summary
This summary is machine-generated.

The PHAge Search Tool (PHAST) quickly and accurately identifies prophage sequences in bacterial genomes. This tool enhances prophage detection speed and sensitivity for genomic analysis.

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Last Updated: Jun 1, 2026

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Published on: May 22, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Microbiology

Background:

  • Bacterial genomes frequently harbor prophage sequences, which are integrated viral DNA.
  • Accurate identification and annotation of prophages are crucial for understanding bacterial evolution and phage-host interactions.
  • Existing tools for prophage detection can be slow and lack comprehensive annotation capabilities.

Purpose of the Study:

  • To develop a rapid and accurate web server for identifying, annotating, and visualizing prophage sequences in bacterial genomes.
  • To improve upon the speed and sensitivity of existing prophage detection methods.
  • To provide detailed annotation of prophage features and distinguish between intact and incomplete prophages.

Main Methods:

  • The PHAge Search Tool (PHAST) web server was developed using database comparisons and phage 'cornerstone' feature identification.
  • PHAST accepts raw DNA sequence data or GenBank formatted data as input.
  • The tool performs rapid analysis to locate, annotate, and display prophage sequences and their features.

Main Results:

  • PHAST demonstrates significant improvements in speed, being up to 40 times faster than other prophage identification tools.
  • PHAST exhibits increased sensitivity, detecting up to 15% more prophage sequences.
  • The tool provides richly annotated tables, distinguishes between intact and incomplete prophages, and generates high-quality interactive graphics.

Conclusions:

  • PHAST is a highly efficient and sensitive web server for prophage identification and annotation in bacterial genomes.
  • The tool's ability to process diverse input formats and provide detailed graphical outputs makes it valuable for genomic research.
  • PHAST offers a significant advancement in the analysis of prophage elements within bacterial DNA sequences.