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PHASTEST: faster than PHASTER, better than PHAST
Open accessAbstract
PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports rapid annotation and interactive visualization of all other genes (protein coding regions, tRNA/tmRNA/rRNA sequences) in bacterial genomes. Given that bacterial genome sequencing has become so routine, the need for fast tools to comprehensively annotate bacterial genomes has become progressively more important. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors, it also provides more complete whole genome annotations and much improved genome visualization capabilities. In standardized tests, we found that PHASTEST is 31% faster and 2–3% more accurate in prophage identification than PHASTER. Specifically, PHASTEST can process a typical bacterial genome in 3.2 min (raw sequence) or in 1.3 min when given a pre-annotated GenBank file. Improvements in PHASTEST’s ability to annotate bacterial genomes now make it a particularly powerful tool for whole genome annotation. In addition, PHASTEST now offers a much more modern and responsive visualization interface that allows users to generate, edit, annotate and interactively visualize (via zooming, rotating, dragging, panning, resetting), colourful, publication quality genome maps. PHASTEST continues to offer popular options such as an API for programmatic queries, a Docker image for local installations, support for multiple (metagenomic) queries and the ability to perform automated look-ups against thousands of previously PHAST-annotated bacterial genomes. PHASTEST is available online at https://phastest.ca.
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Cites
Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175
Cited by
Humolli, D., Piel, D., Maffei, E., Heyer, Y., Agustoni, E., Shaidullina, A., Willi, L., Imwinkelried, P., Estermann, F., Cuénod, A., et al. (2025) · PLOS Biology · doi:10.1371/journal.pbio.3003063 · Cited by 36
Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes
Heyer, R., Wolf, M., Benndorf, D., Uzzau, S., Seifert, J., Grenga, L., Pabst, M., Schmitt, H., Mesuere, B., Van Den Bossche, T., et al. (2025) · Microbiome · doi:10.1186/s40168-025-02119-5 · Cited by 22
Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts
Chen, J., Nilsen, E. D., Chitboonthavisuk, C., Corban, J. E., Yang, M., Mo, C. Y., & Raman, S. (2025) · Cell Host & Microbe · doi:10.1016/j.chom.2025.06.018 · Cited by 16
Di Pierro, F., Sagheddu, V., Galletti, S., Casaroli, A., Labrini, E., Soldi, S., Cazzaniga, M., Bertuccioli, A., Matera, M., Cavecchia, I., et al. (2026) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10522-5 · Cited by 5
“The PHASTEST tool (Phage Search Tool for Escherichia coli ), a freely accessible [100] and user-friendly online tool that can identify and classify prophages and other phage-related sequences in bacterial genomes, was used to detect phage sequences in the E. coli genomes [101].”
Sliti, A., Kim, R.-H., Lee, D., & Shin, J.-H. (2025) · Microbial Pathogenesis · doi:10.1016/j.micpath.2025.107405 · Cited by 5
Metadata
- Authors
- Wishart, D. S., Han, S., Saha, S., Oler, E., Peters, H., Grant, J. R., Stothard, P., & Gautam, V.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-05-17
- Volume
- 51
- Issue
- W1
- Pages
- W443-W450
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4376871556
- Cited by
- 647
- References
- 1
- FWCI
- 102.95
- Type
- journal article
- Language
- en
- Open access
- gold
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- Wishart, D. S., Han, S., Saha, S., Oler, E., Peters, H., Grant, J. R., Stothard, P., & Gautam, V. (2023). PHASTEST: faster than PHASTER, better than PHAST. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad382
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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