Frontiers in Genetics (Dec 2018)

PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes

  • Ailton Lopes de Sousa,
  • Dener Maués,
  • Amália Lobato,
  • Edian F. Franco,
  • Kenny Pinheiro,
  • Fabrício Araújo,
  • Yan Pantoja,
  • Artur Luiz da Costa da Silva,
  • Jefferson Morais,
  • Rommel T. J. Ramos

DOI
https://doi.org/10.3389/fgene.2018.00644
Journal volume & issue
Vol. 9

Abstract

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This study developed a computational tool with a graphical interface and a web-service that allows the identification of phage regions through homology search and gene clustering. It uses G+C content variation evaluation and tRNA prediction sites as evidence to reinforce the presence of prophages in indeterminate regions. Also, it performs the functional characterization of the prophages regions through data integration of biological databases. The performance of PhageWeb was compared to other available tools (PHASTER, Prophinder, and PhiSpy) using Sensitivity (Sn) and Positive Predictive Value (PPV) tests. As a reference for the tests, more than 80 manually annotated genomes were used. In the PhageWeb analysis, the Sn index was 86.1% and the PPV was approximately 87%, while the second best tool presented Sn and PPV values of 83.3 and 86.5%, respectively. These numbers allowed us to observe a greater precision in the regions identified by PhageWeb while compared to other prediction tools submitted to the same tests. Additionally, PhageWeb was much faster than the other computational alternatives, decreasing the processing time to approximately one-ninth of the time required by the second best software. PhageWeb is freely available at http://computationalbiology.ufpa.br/phageweb.

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