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AMRFinder Version 1

NCBI has developed AMRFinder, a tool that identifies AMR genes using either protein annotations or nucleotide sequence. AMRFinder is used in the Pathogen Detection pipeline, and these data are displayed in NCBI’s Isolate Browser. AMRFinder can identify acquired antimicrobial resistance genes in either protein datasets or nucleotide data, including genomic data. AMRFinder relies on NCBI’s curated AMR gene database and curated collection of Hidden Markov Models. For more information on how AMRFinder operates, please see the Methods section of the AMRFinder wiki.

To enable researchers to incorporate these tools into their own analytical pipelines, NCBI has made the following resources publicly available:

  1. A downloadable version of AMRFinder for Linux. See the wiki for installation instructions.
  2. NCBI’s Bacterial Antimicrobial Resistance Reference Gene Database, which contains over 4,000 curated AMR protein sequences. There is now a table-based browser for the reference gene/protein set available: NCBI Reference Gene Browser.
  3. NCBI’s curated HMM collection of AMR protein sequences.

Note that this version of AMRFinder is a version 1. If you have any questions about or experience problems running AMRFinder, please contact pd-help@ncbi.nlm.nih.gov