PlasmidFinder

PlasmidFinder is a tool for detecting plasmid sequences in whole genome data, primarily from Enterobacteriaceae. It is described in:

  • Carattoli et al. 2014 In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895-903. https://pubmed.ncbi.nlm.nih.gov/24777092/

  • Carattoli et al. 2020 PlasmidFinder and in silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS) Methods Mol Biol 2075:285-294. https://pubmed.ncbi.nlm.nih.gov/31584170/

The function can be accessed by selecting the ‘Analysis’ section on the main contents page.

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Jump to the ‘Third party’ category, follow the link to PlasmidFinder, then click ‘Launch PlasmidFinder’.

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Alternatively, it can be accessed following a query by clicking the ‘PlasmidFinder’ button in the ‘Third party’ list at the bottom of the results table. Please note that the list of functions here may vary depending on the setup of the database.

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Select the isolate records to analyse - these will be pre-selected if you accessed the plugin following a query.

Click submit.

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The analysis will be submitted to the job queue.

If plasmids are found, these are displayed in a table as output. There will also be an output file containing the results. This will either be a single JSON file, or a zip file containing multiple JSON files if more than one isolate was selected.

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If plasmids are found, these results are stored within the database and will be displayed with an isolate record for anybody accessing it in the future.

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