ArticlePLoS computational biology2020
Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation.
Article in PLoS computational biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
- The complete genome sequence ofMicrobiology resource announcements · 2026Article
- Isolation, characterization, and genomic analysis of a novel lytic bacteriophage with potent antibiofilm activity against multidrug-resistant Acinetobacter baumannii.BMC microbiology · 2026Article
- Complete genome sequence ofMicrobiology resource announcements · 2026Article
- Evolutionary interplay: virulence, endolysin-like hydrolases, and defense correlations in the Erwinia amylovora pangenome.BMC microbiology · 2026Article
- Genomic analysis of prophages from Burkholderia gladioli exposes extensive genetic diversity.BMC genomics · 2026Article
- PRISM: A unified platform for phage isolation and characterization from single-droplet microenvironments.Science advances · 2026Article
- Unveiling Novel Lytic Bacteriophages as Natural Biocontrol Agents Against Multidrug-Resistant Escherichia coli: Isolation, Characterization, and In vitro Application.Food and environmental virology · 2026Article
- Exploring the Antibacterial Properties of a Newly Isolated Microviridae Phage Against Multidrug-ResistantPathogens (Basel, Switzerland) · 2026Article
- Resolution of a T1-Like Bacteriophage Outbreak by Receptor Engineering.Molecular biotechnology · 2026Article
- Isolation, characterization and genomic analysis of a novel lytic bacteriophage EcoPhCCP1, capable of infecting multiple strains of multidrug-resistantThe Journal of general virology · 2026Article
- Isolation and characterization of TayeBlu, a novel bacteriophage ofMicrobiology spectrum · 2026Article
- The complete genome ofMicrobiology resource announcements · 2025Article
- Isolation and characterization of biofilm-disrupting proteus phage Premi.Scientific reports · 2025Article
- Phage N4 uses a SAR endolysin-holin system for host cell lysis.bioRxiv : the preprint server for biology · 2025Article
- Isolation and characterization of an antibiofilm bacteriophage against Klebsiella michiganensis and evaluation of its therapeutic potential in an insect larval gut colonization model.BMC microbiology · 2025Article
- Article
- Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut.Virology journal · 2025Article
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- Characterization and purification of Pseudomonas aeruginosa phages for the treatment of canine infections.BMC microbiology · 2025Article
- Mystique, a broad host range Acinetobacter phage, reveals the impact of culturing conditions on phage isolation and infectivity.PLoS pathogens · 2025Article
57 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
In the modern genomic era, scientists without extensive bioinformatic training need to apply high-power computational analyses to critical tasks like phage genome annotation. At the Center for Phage Technology (CPT), we developed a suite of phage-oriented tools housed in open, user-friendly web-based interfaces. A Galaxy platform conducts computationally intensive analyses and Apollo, a collaborative genome annotation editor, visualizes the results of these analyses. The collection includes open source applications such as the BLAST+ suite, InterProScan, and several gene callers, as well as unique tools developed at the CPT that allow maximum user flexibility. We describe in detail programs for finding Shine-Dalgarno sequences, resources used for confident identification of lysis genes such as spanins, and methods used for identifying interrupted genes that contain frameshifts or introns. At the CPT, genome annotation is separated into two robust segments that are facilitated through the automated execution of many tools chained together in an operation called a workflow. First, the structural annotation workflow results in gene and other feature calls. This is followed by a functional annotation workflow that combines sequence comparisons and conserved domain searching, which is contextualized to allow integrated evidence assessment in functional prediction. Finally, we describe a workflow used for comparative genomics. Using this multi-purpose platform enables researchers to easily and accurately annotate an entire phage genome. The portal can be accessed at https://cpt.tamu.edu/galaxy-pub with accompanying user training material.
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