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 …
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 …
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 …
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 …
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 …
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 …
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 …
[HTML][HTML] PhageScope: a well-annotated bacteriophage database with automatic analyses and visualizations
Bacteriophages are viruses that infect bacteria or archaea. Understanding the diverse and
intricate genomic architectures of phages is essential to study microbial ecosystems and …
intricate genomic architectures of phages is essential to study microbial ecosystems and …
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 …
Prophinder: a computational tool for prophage prediction in prokaryotic genomes
G Lima-Mendez, J Van Helden, A Toussaint… - …, 2008 - academic.oup.com
Prophinder is a prophage prediction tool coupled with a prediction database, a web server
and web service. Predicted prophages will help to fill the gaps in the current sparse phage …
and web service. Predicted prophages will help to fill the gaps in the current sparse phage …