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Title: Predicting promoters in phage genomes using PhagePromoter

Abstract

Abstract Summary The growing interest in phages as antibacterial agents has led to an increase in the number of sequenced phage genomes, increasing the need for intuitive bioinformatics tools for performing genome annotation. The identification of phage promoters is indeed the most difficult step of this process. Due to the lack of online tools for phage promoter prediction, we developed PhagePromoter, a tool for locating promoters in phage genomes, using machine learning methods. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs. Availability and implementation This tool was integrated in the Galaxy framework and it is available online at: https://bit.ly/2Dfebfv. Supplementary information Supplementary data are available at Bioinformatics online.

Authors:
 [1]; ORCiD logo [1];  [1]; ORCiD logo [1];
  1. Centre of Biological Engineering, School of Engineering, University of Minho, Braga, Portugal
Publication Date:
Sponsoring Org.:
USDOE Office of Nuclear Energy (NE), Fuel Cycle Technologies (NE-5)
OSTI Identifier:
1582461
Grant/Contract Number:  
UID/BIO/04469/2019; POCI-01-0145-FEDER-029628; NORTE-01-0145-FEDER-000004
Resource Type:
Published Article
Journal Name:
Bioinformatics
Additional Journal Information:
Journal Name: Bioinformatics Journal Volume: 35 Journal Issue: 24; Journal ID: ISSN 1367-4803
Publisher:
Oxford University Press
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Sampaio, Marta, Rocha, Miguel, Oliveira, Hugo, Dias, Oscar, and Valencia, ed., Alfonso. Predicting promoters in phage genomes using PhagePromoter. United Kingdom: N. p., 2019. Web. doi:10.1093/bioinformatics/btz580.
Sampaio, Marta, Rocha, Miguel, Oliveira, Hugo, Dias, Oscar, & Valencia, ed., Alfonso. Predicting promoters in phage genomes using PhagePromoter. United Kingdom. doi:10.1093/bioinformatics/btz580.
Sampaio, Marta, Rocha, Miguel, Oliveira, Hugo, Dias, Oscar, and Valencia, ed., Alfonso. Mon . "Predicting promoters in phage genomes using PhagePromoter". United Kingdom. doi:10.1093/bioinformatics/btz580.
@article{osti_1582461,
title = {Predicting promoters in phage genomes using PhagePromoter},
author = {Sampaio, Marta and Rocha, Miguel and Oliveira, Hugo and Dias, Oscar and Valencia, ed., Alfonso},
abstractNote = {Abstract Summary The growing interest in phages as antibacterial agents has led to an increase in the number of sequenced phage genomes, increasing the need for intuitive bioinformatics tools for performing genome annotation. The identification of phage promoters is indeed the most difficult step of this process. Due to the lack of online tools for phage promoter prediction, we developed PhagePromoter, a tool for locating promoters in phage genomes, using machine learning methods. This is the first online tool for predicting promoters that uses phage promoter data and the first to identify both host and phage promoters with different motifs. Availability and implementation This tool was integrated in the Galaxy framework and it is available online at: https://bit.ly/2Dfebfv. Supplementary information Supplementary data are available at Bioinformatics online.},
doi = {10.1093/bioinformatics/btz580},
journal = {Bioinformatics},
number = 24,
volume = 35,
place = {United Kingdom},
year = {2019},
month = {7}
}

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