The DOI matches its Crossref record; 18 of the 18 references it cites were found in a registry or an index.
IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.
Open accessAbstract
IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a widely used web-based resource for the prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin, and are of high interest since they disproportionately encode genes involved in medically and environmentally important adaptations, including antimicrobial resistance and virulence. We now report a major new release of IslandViewer, since the last release in 2013. IslandViewer 3 incorporates a completely new genome visualization tool, IslandPlot, enabling for the first time interactive genome analysis and gene search capabilities using synchronized circular, horizontal and vertical genome views. In addition, more curated virulence factors and antimicrobial resistance genes have been incorporated, and homologs of these genes identified in closely related genomes using strict filters. Pathogen-associated genes have been re-calculated for all pre-computed complete genomes. For user-uploaded genomes to be analysed, IslandViewer 3 can also now handle incomplete genomes, with an improved queuing system on compute nodes to handle user demand. Overall, IslandViewer 3 represents a significant new version of this GI analysis software, with features that may make it more broadly useful for general microbial genome analysis and visualization.
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Cites
The Comprehensive Antibiotic Resistance Database
McArthur, A. G., Waglechner, N., Nizam, F., Yan, A., Azad, M. A., Baylay, A. J., Bhullar, K., Canova, M. J., De Pascale, G., Ejim, L., et al. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00419-13 · Cited by 2,226
Self-citationPathogenicity Islands and the Evolution of Microbes
Hacker, J., & Kaper, J. B. (2000) · Annual Review of Microbiology · doi:10.1146/annurev.micro.54.1.641 · Cited by 1,303
ARDB--Antibiotic Resistance Genes Database
Liu, B., & Pop, M. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn656 · Cited by 1,257
PATRIC, the bacterial bioinformatics database and analysis resource
Wattam, A. R., Abraham, D., Dalay, O., Disz, T. L., Driscoll, T., Gabbard, J. L., Gillespie, J. J., Gough, R., Hix, D., Kenyon, R., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1099 · Cited by 1,243
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
Hacker, J., & Carniel, E. (2001) · EMBO reports · doi:10.1093/embo-reports/kve097 · Cited by 620
Reordering contigs of draft genomes using the Mauve Aligner
Rissman, A. I., Mau, B., Biehl, B. S., Darling, A. E., Glasner, J. D., & Perna, N. T. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp356 · Cited by 579
Chen, L., Xiong, Z., Sun, L., Yang, J., & Jin, Q. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr989 · Cited by 541
Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models
Waack, S., Keller, O., Asper, R., Brodag, T., Damm, C., Fricke, W. F., Surovcik, K., Meinicke, P., & Merkl, R. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-142 · Cited by 392
IslandPath: aiding detection of genomic islands in prokaryotes
Hsiao, W., Wan, I., Jones, S. J., & Brinkman, F. S. L. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg004 · Cited by 388
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Cited by
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets
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) · Nucleic Acids Research · doi:10.1093/nar/gkx343 · Cited by 1,543
Self-citationWinsor, G. L., Griffiths, E. J., Lo, R., Dhillon, B. K., Shay, J. A., & Brinkman, F. S. L. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1227 · Cited by 1,050
Self-citationGroß, U., Brzuszkiewicz, E., Gunka, K., Starke, J., Riedel, T., Bunk, B., Spröer, C., Wetzel, D., Poehlein, A., Chibani, C., et al. (2018) · BMC Genomics · doi:10.1186/s12864-017-4368-0 · Cited by 687
Maguire, F., Jia, B., Gray, K. L., Lau, W. Y. V., Beiko, R. G., & Brinkman, F. S. L. (2020) · Microbial Genomics · doi:10.1099/mgen.0.000436 · Cited by 152
“Thirty RefSeq genomes were selected using IslandPath-DIMOB [40] GI prediction data collated into the Island-Viewer database ( www. pathogenomics. sfu. ca/ islandviewer) [41] (Table S1, available with the online version of this article).”
Self-citationIdentification of an operon involved in fluoride resistance in Enterobacter cloacae FRM
Liu, X., Tian, J., Liu, L., Zhu, T., Yu, X., Chu, X., Yao, B., Wu, N., & Fan, Y. (2017) · Scientific Reports · doi:10.1038/s41598-017-06988-1 · Cited by 17
Metadata
- Authors
- Dhillon, B. K., Laird, M. R., Shay, J. A., Winsor, G. L., Lo, R., Nizam, F., Pereira, S. K., Waglechner, N., McArthur, A. G., Langille, M. G. I., & Brinkman, F. S. L.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-04-27
- Volume
- 43
- Issue
- W1
- Pages
- W104-W108
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W1967779392
- Cited by
- 266
- References
- 18
- FWCI
- 26.37
- Type
- journal article
- Language
- en
- Open access
- gold
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- Dhillon, B. K., Laird, M. R., Shay, J. A., Winsor, G. L., Lo, R., Nizam, F., Pereira, S. K., Waglechner, N., McArthur, A. G., Langille, M. G. I., & Brinkman, F. S. L. (2015). IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1. Nucleic Acids Research. https://doi.org/10.1093/nar/gkv401
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