CARD Variants Download README

Use or reproduction of these materials, in whole or in part, by any non-academic 
organization whether or not for non-commercial (including research) or commercial purposes
is prohibited, except with written permission of McMaster University. Commercial uses are
offered only pursuant to a written license and user fee. To obtain permission and begin 
the licensing process, see http://card.mcmaster.ca/about.

For details on how these data are generated, see https://card.mcmaster.ca/genomes and
https://card.mcmaster.ca/prevalence.

FASTA:

Nucleotide and corresponding protein FASTA downloads are available as separate files for 
each model type.  For example, the "protein homolog" model type contains sequences of
antimicrobial resistance genes that do not include mutation as a determinant of resistance
- these data are appropriate for BLAST analysis of metagenomic data or searches excluding 
secondary screening for resistance mutations. In contrast, the "protein variant" model 
includes reference wild type sequences used for mapping SNPs conferring antimicrobial 
resistance - without secondary mutation screening, analyses using these data will include 
false positives for antibiotic resistant gene variants or mutants. 

INDEX FILES:

The file "index-for-model-sequences.txt" contains all the detection statistics for the 
sequences available in the above FASTA files, indicating pathogen, detection criteria, 
ARO categorization, and similarity to curated CARD reference sequence.

The file "card_prevalence.txt" gives prevalence statistics based on the contents of 
"index-for-model-sequences.txt" corresponding to those found at 
https://card.mcmaster.ca/prevalence.
