ReviewMicrobiology and molecular biology reviews : MMBR2022
Computational Tools for the Analysis of Uncultivated Phage Genomes.
Review in Microbiology and molecular biology reviews : MMBR, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Gut virome dynamics: from commensal to critical player in health and disease.Nature reviews. Gastroenterology & hepatology · 2026Review
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- Extensive hidden prophage diversity inMicrobiology (Reading, England) · 2026Article
- Translational barriers to phage endolysin deployment for antimicrobial resistance control in Africa.Frontiers in antibiotics · 2026Review
- DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.bioRxiv : the preprint server for biology · 2025Article
- Protein Set Transformer: a protein-based genome language model to power high-diversity viromics.Nature communications · 2025Article
- Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.Briefings in bioinformatics · 2025Review
- Dual Nature of Bacteriophages: Friends or Foes in Minimally Processed Food Products-A Comprehensive Review.Viruses · 2025Review
- Bacteriophages: A Challenge for Antimicrobial Therapy.Microorganisms · 2025Review
- Geographic variation in abundance and diversity ofFrontiers in microbiology · 2025Article
- Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses.Microorganisms · 2024Article
- Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont.Nature communications · 2024Article
- Benchmarking informatics approaches for virus discovery: caution is needed when combiningmSystems · 2024Article
- Fully Characterized Effective Bacteriophages Specific against Antibiotic-ResistantMedicina (Kaunas, Lithuania) · 2024Article
- Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches.Current opinion in microbiology · 2024Review
- Article
- Tools and methodology toFrontiers in microbiology · 2024Review
- Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses.Methods in molecular biology (Clifton, N.J.) · 2024Article
- KEGG tools for classification and analysis of viral proteins.Protein science : a publication of the Protein Society · 2023Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity.
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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.