PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
S Akhter, RK Aziz, RA Edwards - Nucleic acids research, 2012 - academic.oup.com
Prophages are phages in lysogeny that are integrated into, and replicated as part of, the
host bacterial genome. These mobile elements can have tremendous impact on their …
host bacterial genome. These mobile elements can have tremendous impact on their …
Prophage Hunter: an integrative hunting tool for active prophages
Identifying active prophages is critical for studying coevolution of phage and bacteria,
investigating phage physiology and biochemistry, and engineering designer phages for …
investigating phage physiology and biochemistry, and engineering designer phages for …
Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences
M Bose, RD Barber - In silico biology, 2006 - content.iospress.com
Prophage loci often remain under-annotated or even unrecognized in prokaryotic genome
sequencing projects. A PHP application, Prophage Finder, has been developed and …
sequencing projects. A PHP application, Prophage Finder, has been developed and …
PHAST, PHASTER and PHASTEST: tools for finding prophage in bacterial genomes
D Arndt, A Marcu, Y Liang… - Briefings in …, 2019 - academic.oup.com
Abstract PHAST (PHAge Search Tool) and its successor PHASTER (PHAge Search Tool–
Enhanced Release) have become two of the most widely used web servers for identifying …
Enhanced Release) have become two of the most widely used web servers for identifying …
PHAST: a fast phage search tool
Y Zhou, Y Liang, KH Lynch, JJ Dennis… - Nucleic acids …, 2011 - academic.oup.com
Abstract PHAge Search Tool (PHAST) is a web server designed to rapidly and accurately
identify, annotate and graphically display prophage sequences within bacterial genomes or …
identify, annotate and graphically display prophage sequences within bacterial genomes or …
Rapid discovery of novel prophages using biological feature engineering and machine learning
Prophages are phages that are integrated into bacterial genomes and which are key to
understanding many aspects of bacterial biology. Their extreme diversity means they are …
understanding many aspects of bacterial biology. Their extreme diversity means they are …
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
DE Fouts - Nucleic acids research, 2006 - academic.oup.com
Phage_Finder, a heuristic computer program, was created to identify prophage regions in
completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose …
completed bacterial genomes. Using a test dataset of 42 bacterial genomes whose …
Computational tools for the analysis of uncultivated phage genomes
JS Andrade-Martínez, LC Camelo Valera… - Microbiology and …, 2022 - Am Soc Microbiol
Over a century of bacteriophage research has uncovered a plethora of fundamental aspects
of their biology, ecology, and evolution. Furthermore, the introduction of community-level …
of their biology, ecology, and evolution. Furthermore, the introduction of community-level …
Phigaro: high-throughput prophage sequence annotation
EV Starikova, PO Tikhonova, NA Prianichnikov… - …, 2020 - academic.oup.com
Phigaro is a standalone command-line application that is able to detect prophage regions
taking raw genome and metagenome assemblies as an input. It also produces dynamic …
taking raw genome and metagenome assemblies as an input. It also produces dynamic …
Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and …
KA Kleinheinz, KG Joensen, MV Larsen - Bacteriophage, 2014 - Taylor & Francis
Extensive research is currently being conducted on the use of bacteriophages for
applications in human medicine, agriculture and food manufacturing. However, phages are …
applications in human medicine, agriculture and food manufacturing. However, phages are …