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

Part of the Methods in Molecular Biology book series (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.

Key words

Orthologs Paralogs Pan-genomics Comparative genomics Bacterial genomes pIncA/C plasmids Core-genome Pan-genome Software Open-source 

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Centro de Ciencias GenómicasUniversidad Nacional Autónoma de MéxicoCuernavaca, MorelosMexico
  2. 2.Estación Experimental de Aula DeiConsejo Superior de Investigaciones Científicas (EEAD-CSIC)ZaragozaSpain
  3. 3.Fundación ARAIDZaragozaSpain

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