RGI Resistance Gene Identifier

RGI Bulk Analysis: Do you want to use RGI to analyze a large number of genomes? It is now available as a downloadable command-line tool in the Download section of the CARD website.

RGI 4.2.2, CARD 3.0.0: Open Reading Frame (ORF) prediction using Prodigal, homolog detection using Diamond, and Strict significance based on CARD curated bitscore cut-offs. Addition of rRNA mutation and efflux over-expression models. Hits of 95% identity or better are automatically listed as Strict. All results organized by revised ARO classification: AMR Gene Family, Drug Class, and Resistance Mechanism. Support added for low quality/coverage assemblies, metagenomic merged reads, small plasmids or assembly contigs.

Online RGI results cached for 7 days. As the CARD curation evolves, the results of the RGI evolve. RGI targets, reference sequences, and significance cut-offs are under constant curation.

If DNA sequences are submitted, RGI first predicts complete open reading frames using Prodigal (ignoring those less than 30 bp) and analyzes the predicted protein sequences. RGI cannot currently analyze individual metagenomics sequence reads, but can analyze metagenomic assembly contigs or merged metagenomic reads using Prodigal's algorithms for low quality/coverage assemblies and inclusion of partial gene prediction. If the low sequence quality option is selected, RGI uses Prodigal anonymous mode for open reading frame prediction, supporting calls of partial AMR genes from short or low quality contigs.

The RGI currently supports protein homolog models (use of sequence similarity cut-offs to detection functional homologs of AMR genes), protein variant models (for accurate differentiation between susceptible intrinsic genes and intrinsic genes that have acquired mutations conferring AMR, based on curated SNP matrices), rRNA mutation models (for detection of drug resistant rRNA target sequences), and protein over-expression models (which detect efflux subunits associated AMR, but also highlights mutations conferring over-expression when present). For more details, see the Model Ontology

The RGI analyzes sequences under three paradigms – Perfect, Strict, and Loose (a.k.a. Discovery). The Perfect algorithm is most often applied to clinical surveillance as it detects perfect matches to the curated reference sequences and mutations in the CARD. In contrast, the Strict algorithm detects previously unknown variants of known AMR genes, including secondary screen for key mutations, using detection models with curated similarity cut-offs to ensure the detected variant is likely a functional AMR gene. The Loose algorithm works outside of the detection model cut-offs to provide detection of new, emergent threats and more distant homologs of AMR genes, but will also catalog homologous sequences and spurious partial hits that may not have a role in AMR. Combined with phenotypic screening, the Loose algorithm allows researchers to hone in on new AMR genes.

Use RGI:

Nucleotide sequences will undergo ORF calling to generate predicted protein sequences. Examples: JN420336.1, AY123251.1, HQ451074.1, AL123456

Upload a plain text file containing DNA or protein sequence(s) in FASTA format (20 Mb limit). The file can contain more than one FASTA formatted sequence, such as assembly contigs or multiple proteins. Each file will be treated as a single sample.

1 Complete genomes, plasmids, or high quality assemblies (includes contigs > 20,000 bp). Excludes prediction of partial genes.
2 Low quality/coverage assemblies, metagenomic merged reads, small plasmids or assembly contigs (<20,000 bp). Includes prediction of partial genes.

Upload external RGI json results and visualize:

Upload a JSON file containing RGI results generated using the command-line version. File size limited to 20 Mb. Note that only Loose hits of e-10 or better can be visualized.

Upload JSON