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CCB-SB / plsdb

PLSDB pipeline to collect bacterial plasmids from NCBI
https://ccb-microbe.cs.uni-saarland.de/plsdb/
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Resistance genes information #23

Closed mdiricks closed 1 year ago

mdiricks commented 1 year ago

Dear PLSDB team, Where can you find information on the resistance genes found on the plasmids? And with which thresholds are these genes evaluated (gene coverage and identity). Kind regards,

mdiricks commented 1 year ago

Found it: You need to click on the plasmid in the overview table to get into the specific plasmid overview. Resistance genes are then mentioned (only if found) in the Additional annotations section (see e.g. https://ccb-microbe.cs.uni-saarland.de/plsdb/plasmids/plasmid/NC_017908.2/).

Tresholds are unclear though.

VGalata commented 1 year ago

Hi @mdiricks,

We use abricate for resistance annotations and the thresholds can be found here in the workflow config.

Best wishes, Valentina