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Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: A case study of pIncA/C plasmids

Autor Vinuesa, Pablo; Contreras-Moreira, Bruno
Palabras clave Orthologs
Comparative genomics
Bacterial genomes
pIncA/C plasmids
Fecha de publicación 2015
Citación Vinuesa P, Contreras-Moreira B. 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 and protocols. Methods in Molecular Biology 1231: 203-232 (2015)
ResumenGET_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.
Descripción 35 Pags.- 5 Figs. The definitive version is available at: http://link.springer.com/book/10.1007/978-1-4939-1720-4
Versión del editorhttp://dx.doi.org/10.1007/978-1-4939-1720-4_14
URI http://hdl.handle.net/10261/108698
ISBN 978-1-4939-1719-8
Referencias978-1-4939-1720-4 (E-ISBN)
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