ArticleG3 (Bethesda, Md.)2021
MultiPhATE2: code for functional annotation and comparison of phage genomes.
Article in G3 (Bethesda, Md.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Innovative Applications of Artificial Intelligence in Bacteriophage Research: A New Chapter in Future Medicine.Microorganisms · 2026Review
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- The epidermal ecotone: a proposed model system for marine viral ecology at the animal-environmental interface.NPJ biofilms and microbiomes · 2026Review
- Extensive cultivation of human gut phages revealing undescribedGut microbes · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Genetic Code-Locking Confers Stable Virus Resistance to a Recoded Organism.Biochemistry · 2025Article
- Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium.Scientific reports · 2024Article
- Isolation and characterization of two novel bacteriophages against carbapenem-resistantFrontiers in cellular and infection microbiology · 2024Article
- Ongoing shuffling of protein fragments diversifies core viral functions linked to interactions with bacterial hosts.Nature communications · 2023Article
- Knowing and Naming: Phage Annotation and Nomenclature for Phage Therapy.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2023Review
- The phageome in normal and inflamed human skin.Science advances · 2023Article
- High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community.mSystems · 2023Article
- Article
- Pharokka: a fast scalable bacteriophage annotation tool.Bioinformatics (Oxford, England) · 2023Article
- Isolation and Characterization of LyticViruses · 2022Article
- Computational Tools for the Analysis of Uncultivated Phage Genomes.Microbiology and molecular biology reviews : MMBR · 2022Review
- Isolation, characterization, molecular analysis and application of bacteriophage DW-EC to control Enterotoxigenic Escherichia coli on various foods.Scientific reports · 2022Article
- APTC-EC-2A: A Lytic Phage Targeting Multidrug ResistantMicroorganisms · 2022Article
- Genomic characterization of bacteriophage BI-EHEC infecting strains of Enterohemorrhagic Escherichia coli.BMC research notes · 2021Article
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Authors and funding
6 authors.
Funding
Abstract
To address a need for improved tools for annotation and comparative genomics of bacteriophage genomes, we developed multiPhATE2. As an extension of multiPhATE, a functional annotation code released previously, multiPhATE2 performs gene finding using multiple algorithms, compares the results of the algorithms, performs functional annotation of coding sequences, and incorporates additional search algorithms and databases to extend the search space of the original code. MultiPhATE2 performs gene matching among sets of closely related bacteriophage genomes, and uses multiprocessing to speed computations. MultiPhATE2 can be re-started at multiple points within the workflow to allow the user to examine intermediate results and adjust the subsequent computations accordingly. In addition, multiPhATE2 accommodates custom gene calls and sequence databases, again adding flexibility. MultiPhATE2 was implemented in Python 3.7 and runs as a command-line code under Linux or MAC operating systems. Full documentation is provided as a README file and a Wiki website.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.