ArticleInternational journal of molecular sciences2019
A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 44 citations in OpenAlex.
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- Hybrid sequencing reveals the genome of a Chrysochromulina parva virus and highlight its distinct replication strategy.BMC genomics · 2025Article
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- Bacteriophages RCF and 1-6bf can control the growth of avian pathogenic Escherichia coli.Poultry science · 2025Article
- Genomic Analysis of 96Viruses · 2025Article
- Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al.PloS one · 2025Article
- Complete genome sequences of cluster F1 and cluster B1Microbiology resource announcements · 2024Article
- Complete genome sequences of cluster G1 and cluster K4Microbiology resource announcements · 2023Article
- Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes.The ISME journal · 2023Article
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- PHERI-Phage Host ExploRation Pipeline.Microorganisms · 2023Article
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- Computational Tools for the Analysis of Uncultivated Phage Genomes.Microbiology and molecular biology reviews : MMBR · 2022Review
- A Novel and Ubiquitous Marine Methylophage Provides Insights into Viral-Host Coevolution and Possible Host-Range Expansion in Streamlined Marine Heterotrophic Bacteria.Applied and environmental microbiology · 2022Article
- Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase.Database : the journal of biological databases and curation · 2022Article
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- Phage Commander, an Application for Rapid Gene Identification in Bacteriophage Genomes Using Multiple Programs.PHAGE (New Rochelle, N.Y.) · 2021Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Bacteriophages are the most numerous entities on Earth. The number of sequenced phage genomes is approximately 8000 and increasing rapidly. Sequencing of a genome is followed by annotation, where genes, start codons, and functions are putatively identified. The mainstays of phage genome annotation are auto-annotation programs such as Glimmer and GeneMark. Due to the relatively small size of phage genomes, many groups choose to manually curate auto-annotation results to increase accuracy. An additional benefit of manual curation of auto-annotated phage genomes is that the process is amenable to be performed by students, and has been shown to improve student recruitment to the sciences. However, despite its greater accuracy and pedagogical value, manual curation suffers from high labor cost, lack of standardization and a degree of subjectivity in decision making, and susceptibility to mistakes. Here, we present a method developed in our lab that is designed to produce accurate annotations while reducing subjectivity and providing a degree of standardization in decision-making. We show that our method produces genome annotations more accurate than auto-annotation programs while retaining the pedagogical benefits of manual genome curation.
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