The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets
Open accessAbstract
IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.
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Cites
Genomic Islands in Pathogenic and Environmental Microorganisms
Dobrindt, U., Hochhut, B., Hentschel, U., & Hacker, J. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro884 · Cited by 1,188
Cited by
Alcock, B. P., Huynh, W., Chalil, R., Smith, K. W., Raphenya, A. R., Wlodarski, M. A., Edalatmand, A., Petkau, A., Syed, S. A., Tsang, K. K., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac920 · Cited by 2,441
Self-citationHost genetic regulation of human gut microbial structural variation
Zhernakova, D. V., Wang, D., Liu, L., Andreu-Sánchez, S., Zhang, Y., Ruiz-Moreno, A. J., Peng, H., Plomp, N., Del Castillo-Izquierdo, Á., Gacesa, R., et al. (2024) · Nature · doi:10.1038/s41586-023-06893-w · Cited by 174
Wang, Y., Liang, Q., Lu, B., Shen, H., Liu, S., Shi, Y., Leptihn, S., Li, H., Wei, J., Liu, C., et al. (2021) · BMC Genomics · doi:10.1186/s12864-021-07539-9 · Cited by 88
Kandasamy, S., Yoo, J., Yun, J., Lee, K.-H., Kang, H.-B., Kim, J.-E., Oh, M.-H., & Ham, J.-S. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232214494 · Cited by 51
Matteoli, F. P., Passarelli-Araujo, H., Pedrosa-Silva, F., Olivares, F. L., & Venancio, T. M. (2020) · Genomics · doi:10.1016/j.ygeno.2019.07.003 · Cited by 27
Metadata
- Authors
- Bertelli, C., Laird, M. R., Williams, K. P., Simon Fraser University Research Computing Group, Lau, B. Y., Hoad, G., Winsor, G. L., & Brinkman, F. S.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-05-02
- Volume
- 45
- Issue
- W1
- Pages
- W30-W35
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2610656577
- Cited by
- 1,543
- References
- 1
- FWCI
- 35.72
- Type
- journal article
- Language
- en
- Open access
- gold
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- Bertelli, C., Laird, M. R., Williams, K. P., Simon Fraser University Research Computing Group, Lau, B. Y., Hoad, G., Winsor, G. L., & Brinkman, F. S. (2017). IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx343
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