The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
PLSDB: a resource of complete bacterial plasmids
Open accessAbstract
The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the number of newly sequenced bacterial genomes is growing a comprehensive resource is required which will allow to browse and filter the available plasmids, and to perform sequence analyses. Here, we present PLSDB, a resource containing 13 789 plasmid records collected from the NCBI nucleotide database. The web server provides an interactive view of all obtained plasmids with additional meta information such as sequence characteristics, sample-related information and taxonomy. Moreover, nucleotide sequence data can be uploaded to search for short nucleotide sequences (e.g. specific genes) in the plasmids, to compare a given plasmid to the records in the collection or to determine whether a sample contains one or multiple of the known plasmids (containment analysis). The resource is freely accessible under https://ccb-microbe.cs.uni-saarland.de/plsdb/.
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Cites
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BLAST+: architecture and applications
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UMAP: Uniform Manifold Approximation and Projection
McInnes, L., Healy, J., Saul, N., & Großberger, L. (2018) · Journal of Open Source Software · doi:10.21105/joss.00861 · Cited by 9,826 · cited 3×
“Then, UMAP was applied to the distance matrix using parameters n neighbors=50, n components=2, init='random', metric='precomputed'.”
MethodInfluentialLiu, Y.-Y., Wang, Y., Walsh, T. R., Yi, L.-X., Zhang, R., Spencer, J., Doi, Y., Tian, G., Dong, B., Huang, X., et al. (2016) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(15)00424-7 · Cited by 5,398
Identification of acquired antimicrobial resistance genes
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Carattoli, A., Zankari, E., García-Fernández, A., Voldby Larsen, M., Lund, O., Villa, L., Møller Aarestrup, F., & Hasman, H. (2014) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02412-14 · Cited by 4,877
Mash: fast genome and metagenome distance estimation using MinHash
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CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database
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Interactive metagenomic visualization in a Web browser
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Cited by
Carvalho, M. J., Sands, K., Thomson, K., Portal, E., Mathias, J., Milton, R., Gillespie, D., Dyer, C., Akpulu, C., Boostrom, I., et al. (2022) · Nature Microbiology · doi:10.1038/s41564-022-01184-y · Cited by 95
IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata
Camargo, A. P., Call, L., Roux, S., Nayfach, S., Huntemann, M., Palaniappan, K., Ratner, A., Chu, K., Mukherjeep, S., Reddy, T. B. K., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkad964 · Cited by 87
Kamathewatta, K., Bushell, R., Rafa, F., Browning, G., Billman-Jacobe, H., & Marenda, M. (2020) · Antimicrobial Resistance & Infection Control · doi:10.1186/s13756-020-00828-0 · Cited by 27
Evolution of a Plasmid Regulatory Circuit Ameliorates Plasmid Fitness Cost
Elg, C. A., Mack, E., Rolfsmeier, M., McLean, T. C., Sneddon, D., Kosterlitz, O., Soderling, E., Narum, S., Rowley, P. A., Sullivan, J., et al. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf062 · Cited by 7
Metadata
- Authors
- Galata, V., Fehlmann, T., Backes, C., & Keller, A.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-10-31
- Volume
- 47
- Issue
- D1
- Pages
- D195-D202
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2909601828
- Cited by
- 470
- References
- 27
- FWCI
- 11.70
- Type
- journal article
- Language
- en
- Open access
- gold
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