The DOI matches its Crossref record; 25 of the 25 references it cites were found in a registry or an index.
Proksee: in-depth characterization and visualization of bacterial genomes
Open accessAbstract
Proksee (https://proksee.ca) provides users with a powerful, easy-to-use, and feature-rich system for assembling, annotating, analysing, and visualizing bacterial genomes. Proksee accepts Illumina sequence reads as compressed FASTQ files or pre-assembled contigs in raw, FASTA, or GenBank format. Alternatively, users can supply a GenBank accession or a previously generated Proksee map in JSON format. Proksee then performs assembly (for raw sequence data), generates a graphical map, and provides an interface for customizing the map and launching further analysis jobs. Notable features of Proksee include unique and informative assembly metrics provided via a custom reference database of assemblies; a deeply integrated high-performance genome browser for viewing and comparing analysis results at individual base resolution (developed specifically for Proksee); an ever-growing list of embedded analysis tools whose results can be seamlessly added to the map or searched and explored in other formats; and the option to export graphical maps, analysis results, and log files for data sharing and research reproducibility. All these features are provided via a carefully designed multi-server cloud-based system that can easily scale to meet user demand and that ensures the web server is robust and responsive.
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Cites
Basic local alignment search tool
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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
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Prokka: rapid prokaryotic genome annotation
Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,818
Circos: An information aesthetic for comparative genomics
Krzywinski, M., Schein, J., Birol, İ., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,964
NCBI prokaryotic genome annotation pipeline
Tatusova, T., DiCuccio, M., Badretdin, A., Chetvernin, V., Nawrocki, E. P., Zaslavsky, L., Lomsadze, A., Pruitt, K. D., Borodovsky, M., & Ostell, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw569 · Cited by 7,014
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018) · Nature Communications · doi:10.1038/s41467-018-07641-9 · Cited by 5,748
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
Alikhan, N.-F., Petty, N. K., Ben Zakour, N. L., & Beatson, S. A. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-402 · Cited by 3,303
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Self-citationDiep, B. A., Gill, S. R., Chang, R. F., Phan, T. H., Chen, J. H., Davidson, M. G., Lin, F., Lin, J., Carleton, H. A., Mongodin, E. F., et al. (2006) · The Lancet · doi:10.1016/s0140-6736(06)68231-7 · Cited by 1,633
Cited by
Chintakovid, N., Singkhamanan, K., Yaikhan, T., Nokchan, N., Wonglapsuwan, M., Jitpakdee, J., Kantachote, D., & Surachat, K. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e33823 · Cited by 26
Agolino, G., Cristofolini, M., Vaccalluzzo, A., Tagliazucchi, D., Cattivelli, A., Pino, A., Caggia, C., Solieri, L., & Randazzo, C. L. (2025) · Biomolecules · doi:10.3390/biom15010086 · Cited by 19
Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components
Duan, C., Liu, Y., Liu, Y., Liu, L., Cai, M., Zhang, R., Zeng, Q., Koonin, E. V., Krupovic, M., & Li, M. (2024) · ISME Communications · doi:10.1093/ismeco/ycad011 · Cited by 7
Sliti, A., Kim, R.-H., Lee, D., & Shin, J.-H. (2025) · Microbial Pathogenesis · doi:10.1016/j.micpath.2025.107405 · Cited by 5
Lu, W., Zha, B., Lyu, J., LingHu, C., Chen, J., Deng, S., Zhang, X., Li, L., & Wang, G. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1500886 · Cited by 4
Metadata
- Authors
- Grant, J. R., Enns, E., Marinier, E., Mandal, A., Herman, E. K., Chen, C.-Y., Graham, M., Van Domselaar, G., & Stothard, P.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2023-05-04
- Volume
- 51
- Issue
- W1
- Pages
- W484-W492
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4368358104
- Cited by
- 1,882
- References
- 25
- FWCI
- 141.14
- Type
- journal article
- Language
- en
- Open access
- gold
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- Grant, J. R., Enns, E., Marinier, E., Mandal, A., Herman, E. K., Chen, C.-Y., Graham, M., Van Domselaar, G., & Stothard, P. (2023). Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad326
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
