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

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...

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Detalles Bibliográficos
Autores principales: de Sousa, Ailton Lopes, Maués, Dener, Lobato, Amália, Franco, Edian F., Pinheiro, Kenny, Araújo, Fabrício, Pantoja, Yan, da Costa da Silva, Artur Luiz, Morais, Jefferson, Ramos, Rommel T. J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305541/
https://www.ncbi.nlm.nih.gov/pubmed/30619469
http://dx.doi.org/10.3389/fgene.2018.00644
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author de Sousa, Ailton Lopes
Maués, Dener
Lobato, Amália
Franco, Edian F.
Pinheiro, Kenny
Araújo, Fabrício
Pantoja, Yan
da Costa da Silva, Artur Luiz
Morais, Jefferson
Ramos, Rommel T. J.
author_facet de Sousa, Ailton Lopes
Maués, Dener
Lobato, Amália
Franco, Edian F.
Pinheiro, Kenny
Araújo, Fabrício
Pantoja, Yan
da Costa da Silva, Artur Luiz
Morais, Jefferson
Ramos, Rommel T. J.
author_sort de Sousa, Ailton Lopes
collection PubMed
description 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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spelling pubmed-63055412019-01-07 PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes de Sousa, Ailton Lopes Maués, Dener Lobato, Amália Franco, Edian F. Pinheiro, Kenny Araújo, Fabrício Pantoja, Yan da Costa da Silva, Artur Luiz Morais, Jefferson Ramos, Rommel T. J. Front Genet Genetics 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. Frontiers Media S.A. 2018-12-18 /pmc/articles/PMC6305541/ /pubmed/30619469 http://dx.doi.org/10.3389/fgene.2018.00644 Text en Copyright © 2018 Sousa, Maués, Lobato, Franco, Pinheiro, Araújo, Pantoja, Costa da Silva, Morais and Ramos. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
de Sousa, Ailton Lopes
Maués, Dener
Lobato, Amália
Franco, Edian F.
Pinheiro, Kenny
Araújo, Fabrício
Pantoja, Yan
da Costa da Silva, Artur Luiz
Morais, Jefferson
Ramos, Rommel T. J.
PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes
title PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes
title_full PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes
title_fullStr PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes
title_full_unstemmed PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes
title_short PhageWeb – Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes
title_sort phageweb – web interface for rapid identification and characterization of prophages in bacterial genomes
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6305541/
https://www.ncbi.nlm.nih.gov/pubmed/30619469
http://dx.doi.org/10.3389/fgene.2018.00644
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