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Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids

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Bacterial Pangenomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1231))

Abstract

GET_HOMOLOGUES is an open-source software package written in Perl and R to define robust core- and pan-genomes by computing consensus clusters of orthologous gene families from whole-genome sequences using the bidirectional best-hit, COGtriangles, and OrthoMCL clustering algorithms. The granularity of the clusters can be fine-tuned by a user-configurable filtering strategy based on a combination of blastp pairwise alignment parameters, hmmscan-based scanning of Pfam domain composition of the proteins in each cluster, and a partial synteny criterion. We present detailed protocols to fit exponential and binomial mixture models to estimate core- and pan-genome sizes, compute pan-genome trees from the pan-genome matrix using a parsimony criterion, analyze and graphically represent the pan-genome structure, and identify lineage-specific gene families for the 12 complete pIncA/C plasmids currently available in NCBI’s RefSeq. The software package, license, and detailed user manual can be downloaded for free for academic use from two mirrors: http://www.eead.csic.es/compbio/soft/gethoms.php and http://maya.ccg.unam.mx/soft/gethoms.php.

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Acknowledgements

We thank Romualdo Zayas, Víctor del Moral, and Alfredo J. Hernández at CCG-UNAM for technical support. We also thank David M. Kristensen and the development team of OrthoMCL for permission to use their code in our project. Funding for this work was provided by the Fundación ARAID, Consejo Superior de Investigaciones Científicas (grant 200720I038), DGAPA-PAPIIT UNAM-México (grant IN211814), and CONACyT-México (grant 179133).

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Authors and Affiliations

  1. Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca, Morelos, Mexico

    Pablo Vinuesa & Bruno Contreras-Moreira

  2. Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas (EEAD-CSIC), Zaragoza, Spain

    Bruno Contreras-Moreira

  3. Fundación ARAID, Zaragoza, Spain

    Bruno Contreras-Moreira

Authors
  1. Pablo Vinuesa
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  2. Bruno Contreras-Moreira
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Corresponding author

Correspondence to Pablo Vinuesa .

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Editors and Affiliations

  1. Department of Biology, University of Florence, Florence, Italy

    Alessio Mengoni

  2. EMBL-EBI, Cambridge, United Kingdom

    Marco Galardini

  3. Department of Biology, University of Florence, Florence, Italy

    Marco Fondi

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Vinuesa, P., Contreras-Moreira, B. (2015). Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids. In: Mengoni, A., Galardini, M., Fondi, M. (eds) Bacterial Pangenomics. Methods in Molecular Biology, vol 1231. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1720-4_14

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  • DOI: https://doi.org/10.1007/978-1-4939-1720-4_14

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1719-8

  • Online ISBN: 978-1-4939-1720-4

  • eBook Packages: Springer Protocols

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