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DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation.

Rui Gan1, FengXia Zhou1, Yu Si1

  • 1HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.

Frontiers in Genetics
|May 6, 2022
PubMed
Summary

DBSCAN-SWA is a new, fast, and accurate command-line tool for identifying prophage regions in bacterial genomes. It demonstrates superior detection power compared to existing methods, aiding genomic and metagenomic analyses.

Keywords:
density-based spatial clusteringphagephage-host interactionprophagesliding window

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Prophages, integrated bacteriophages in bacterial genomes, play a role in horizontal gene transfer (HGT).
  • The increasing volume of microbial genomic and metagenomic data necessitates efficient prophage identification tools.

Purpose of the Study:

  • To develop and introduce DBSCAN-SWA, a novel software tool for rapid and accurate prediction of prophage regions in bacterial genomes.
  • To evaluate the performance of DBSCAN-SWA against existing prophage prediction tools.

Main Methods:

  • DBSCAN-SWA is a command-line software implemented in Python3.
  • Performance was assessed using 184 manually curated prophages for (Multi-) FASTA sequences.
  • Evaluation also included analysis of 19,989 contigs from 400 bacterial genomes from the Human Microbiome Project (HMP).

Main Results:

  • DBSCAN-SWA achieves a recall of 85%, outperforming Phage_Finder (63%), VirSorter (74%), and PHASTER (82%) on curated prophage datasets.
  • The tool demonstrates superior performance on high-throughput sequencing data compared to existing standalone prophage predictors.
  • DBSCAN-SWA offers user-friendly visualizations, including a circular prophage viewer and interactive DataTables.

Conclusions:

  • DBSCAN-SWA provides a faster and more accurate solution for prophage identification in bacterial genomes.
  • The tool is a valuable asset for analyzing large-scale genomic and metagenomic datasets.
  • DBSCAN-SWA is available as open-source software.