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A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation

School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2019, 20(14), 3391;
Received: 30 May 2019 / Revised: 2 July 2019 / Accepted: 9 July 2019 / Published: 10 July 2019
(This article belongs to the Section Molecular Genetics and Genomics)
PDF [1730 KB, uploaded 10 July 2019]


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. View Full-Text
Keywords: bacteriophages; genomics; genome annotation; SEA-PHAGES; Lambda bacteriophages; genomics; genome annotation; SEA-PHAGES; Lambda

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Salisbury, A.; Tsourkas, P.K. A Method for Improving the Accuracy and Efficiency of Bacteriophage Genome Annotation. Int. J. Mol. Sci. 2019, 20, 3391.

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