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Phage Commander, an Application for Rapid Gene Identification in Bacteriophage Genomes Using Multiple Programs.

Matt Lazeroff1, Geordie Ryder2, Sarah L Harris2

  • 1Department of Computer Science, and University of Nevada Las Vegas, Las Vegas, Nevada, USA.

PHAGE (New Rochelle, N.Y.)
|September 23, 2022
PubMed
Summary

Phage Commander integrates multiple gene identification programs to improve bacteriophage genome annotation accuracy. Combining results and manual curation yields the most reliable gene identification for these rapidly growing viral genomes.

Keywords:
bacteriophagesgene identificationgenome annotationgenomics

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Area of Science:

  • Genomics
  • Bioinformatics
  • Microbiology

Background:

  • The exponential growth of sequenced bacteriophage genomes necessitates efficient and accurate gene annotation methods.
  • Current gene identification programs for bacteriophages lack consistent superiority, making program selection challenging.
  • Manual curation is labor-intensive but improves annotation accuracy.

Purpose of the Study:

  • To introduce Phage Commander, an application designed for rapid and integrated bacteriophage gene identification.
  • To facilitate the manual curation process for bacteriophage genome annotations.
  • To benchmark Phage Commander's performance and provide recommendations for optimal annotation strategies.

Main Methods:

  • Phage Commander processes bacteriophage genome sequences through nine gene identification programs and one tRNA identification program.
  • It integrates results into a single table and generates exportable files for GenBank and genome visualization tools.
  • User-defined thresholds can be applied to filter gene export based on program identification consensus.

Main Results:

  • Benchmarking on eight high-quality bacteriophage genomes indicates that exporting genes identified by at least two or three programs yields the most accurate annotations.
  • Manual curation of Phage Commander's output significantly enhances annotation accuracy compared to individual programs.
  • Phage Commander has been shown to reduce labor costs and improve the quality of bacteriophage genome annotations in an educational setting.

Conclusions:

  • Phage Commander effectively integrates multiple gene identification tools for bacteriophage genomics.
  • Manual curation of Phage Commander's integrated output is recommended for achieving maximal annotation accuracy.
  • The application streamlines the annotation process, benefiting both research and education in bacteriophage genomics.