This is the documentation for a Python implementation of a method for searching large metagenomic dataset to identify qnr fluoroquinolone antibiotic resistance genes. It is available online at http://bioinformatics.math.chalmers.se/qnr/.
It uses HMMER3 to search FASTA files of genetic sequences and extracts and classifies hits before clustering them for easier analysis using single-link clustering with NCBI Blastclust.
This pipeline is an implementation of the method described in the paper Boulund et al.: A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences. BMC Genomics 2012 13:695.
The implementation and the latest hidden Markov model is available for download from http://bioinformatics.math.chalmers.se/qnr/download/. The hidden Markov model of the known plasmid-mediated qnr genes is constructed from the list of known qnr alleles listed at http://www.lahey.org/qnrStudies/.