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PHASTEST: faster than PHASTER, better than PHAST.

David S Wishart1,2,3,4, Scott Han1, Sukanta Saha1

  • 1Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.

Nucleic Acids Research
|May 17, 2023
PubMed
Summary

PHASTEST is a new tool for identifying and annotating prophage sequences in bacterial genomes. It offers faster, more accurate results and improved visualization compared to previous tools.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbial genetics

Background:

  • Bacterial genome sequencing is routine, increasing the need for efficient annotation tools.
  • Prophage identification and genome annotation are crucial for understanding bacterial biology.
  • Existing tools like PHAST and PHASTER have limitations in speed and accuracy.

Purpose of the Study:

  • To introduce PHASTEST, a successor to PHAST and PHASTER, for enhanced prophage and gene identification in bacterial genomes.
  • To provide rapid, accurate, and comprehensive annotation and visualization of bacterial genomes.
  • To improve upon the speed, accuracy, and visualization capabilities of previous prophage-finding tools.

Main Methods:

  • PHASTEST was developed as an advancement over PHAST and PHASTER.
  • Standardized tests were conducted to compare PHASTEST's performance against PHASTER.
  • The tool was evaluated for prophage identification accuracy, speed, and whole genome annotation capabilities.

Main Results:

  • PHASTEST is 31% faster and 2-3% more accurate in prophage identification than PHASTER.
  • It processes bacterial genomes rapidly: 3.2 minutes (raw sequence) or 1.3 minutes (GenBank file).
  • PHASTEST provides enhanced whole genome annotation and superior interactive genome visualization.

Conclusions:

  • PHASTEST offers significant improvements in speed, accuracy, and visualization for bacterial genome annotation.
  • It serves as a powerful tool for researchers needing comprehensive analysis of bacterial genomes.
  • The tool supports various features including API access, Docker installation, and metagenomic queries.