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NCBI Antimicrobial Resistance Gene Finder (AMRFinder)

We have a newer version AMRFinderPlus v3.0 that has slightly changed options and significant new features. We are supporting AMRFinder version 1 until AMRFinderPlus is fully tested. If you have issues or concerns please let us know by emailing us at [email protected].

Overview

This software and the accompanying database are designed to find acquired antimicrobial resistance genes in protein or nucleotide sequences.

Installation

AMRFinder requires BLAST, HMMER, and perl. We provide instructions using BioConda to install the prerequisites (and eventually AMRFinder).

Standard installation instructions
Bioconda installation instructions
Compile AMRFinder from source

Mechanism

AMRFinder can be run in two modes with protein sequence as input or with DNA sequence as input. When run with protein sequence it uses both BLASTP and HMMER to search protein sequences for AMR genes along with a hierarchical tree of gene families to classify and name novel sequences. With nucleotide sequences it uses BLASTX translated searches and the hierarchical tree of gene families.

Running AMRFinder
Methods
AMRFinder database

Paper at bioRxiv: Using the NCBI AMRFinder Tool to Determine Antimicrobial Resistance Genotype-Phenotype Correlations Within a Collection of NARMS Isolates

Citation

Feldgarden, Michael, Vyacheslav Brover, Daniel H. Haft, Arjun B. Prasad, Douglas J. Slotta, Igor Tolstoy, Gregory H. Tyson, et al. “Using the NCBI AMRFinder Tool to Determine Antimicrobial Resistance Genotype-Phenotype Correlations Within a Collection of NARMS Isolates.” BioRxiv, February 15, 2019, 550707. https://doi.org/10.1101/550707.

Help

Subscribe to the amrfinder-announce mailing list to get updates when we release new versions of the software or database. This is a low-traffic list.

Note that this version of AMRFinder is an alpha version. If you have any questions about or experience problems running AMRFinder, please contact [email protected].

Licenses