.. Qnr-search Pipeline documentation master file,
   created by Fredrik Boulund (c) 2012

A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences
===============================================================================================================
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. 2012 (submitted).

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/.


Contents:

.. toctree::
   :maxdepth: 2

   introduction
   installation
   pipeline
   usage
   issues
   modifications
   source
   functions
   ack
   changelog
   citing

.. :Authors: 
      Fredrik Boulund,
      Anna Johnning,
      Mariana Pereira,
      Joakim Larsson,
      Erik Kristiansson
    
   :Version: 1.0 of 16 July 2012
    
   :Dedication: 


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`