Abstract
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.
Highlights
Phages are the most abundant organisms on earth (Rohwer, 2003), inhabiting various environments and they are able to infect various bacterial species
Phages are an important factor in bacterial evolution through horizontal gene transfer (Ochman et al, 2000) because they allow the insertion of extrinsic genetic material that can provide new characteristics to their hosts, such as antibiotic resistance, virulence factors, operons or even genomic islands (Bernheim and Sorek, 2018)
It uses the DIAMOND tool (Buchfink et al, 2015) to identify phage-homologous regions in bacterial genomes based on its own database, generating a data table that is integrated into the pipeline
Summary
Phages are the most abundant organisms on earth (Rohwer, 2003), inhabiting various environments and they are able to infect various bacterial species. Phages are an important factor in bacterial evolution through horizontal gene transfer (Ochman et al, 2000) because they allow the insertion of extrinsic genetic material that can provide new characteristics to their hosts, such as antibiotic resistance, virulence factors, operons or even genomic islands (Bernheim and Sorek, 2018). Phages play an ecological role, helping recycle nutrients, and increasing photosynthesis in the oceans (Mann et al, 2003; Sullivan et al, 2003) These organisms have two life cycles: lytic
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