.. IntegronFinder - Detection of Integron in DNA sequences

.. _references:

References
==========

If you use this software, please cite:

- Néron, B.; Littner, E.; Haudiquet, M.; Perrin, A.; Cury, J.; Rocha, E.P.C.
  IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria,
  with a Focus on Antibiotic Resistance in Klebsiella.
  **Microorganisms**, 2022, 10, 700. https://doi.org/10.3390/microorganisms10040700

- Identification and analysis of integrons and cassette arrays in bacterial genomes
  Jean Cury; Thomas Jove; Marie Touchon; Bertrand Neron; Eduardo PC Rocha.
  **Nucleic Acids Research**, 2016; `doi: 10.1093/nar/gkw319 <https://doi.org/10.1093/nar/gkw319/>`_

Please cite also the following articles:

- Nawrocki, E.P. and Eddy, S.R. (2013)
  Infernal 1.1: 100-fold faster RNA homology searches.
  **Bioinformatics**, 29, 2933-2935.

- Eddy, S.R. (2011)
  Accelerated Profile HMM Searches.
  **PLoS Comput Biol**, 7, e1002195.

- Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W. and Hauser, L.J. (2010)
  Prodigal: prokaryotic gene recognition and translation initiation site identification.
  **BMC Bioinformatics**, 11, 119.

and if you use the function `--func_annot` which uses *NCBIfam-AMRFinder* hmm profiles:

 - Haft, DH et al., Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860 PMID: 29112715