PLSDB: a resource of complete bacterial plasmids

PLSDB: a resource of complete bacterial plasmids. Galata, V., Fehlmann, T., Backes, C., & Keller, A. Nucleic acids research, 47:D195-D202, Oxford University Press, October, 2018.
doi abstract bibtex

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/.

@Article{Galata2018,
  author       = {Valentina Galata and Tobias Fehlmann and Christina Backes and Andreas Keller},
  title        = {PLSDB: a resource of complete bacterial plasmids},
  journal      = {Nucleic acids research},
  publisher    = {Oxford University Press},
  year         = {2018},
  volume       = {47},
  issue        = {D1},
  pages        = {D195-D202},
  issn         = {D195-D202},
  issn-linking = {D195-D202},
  month        = oct,
  abstract     = {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/.},
  doi          = {10.1093/nar/gky1050},
  pii          = {10.1093/nar/gky1050},
}

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