title: Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: a case study of pIncA/C plasmids.
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.
authors.affiliation: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, Cuernavaca, Morelos, Mexico, vinuesa@ccg.unam.mx.
authors.forename: Pablo
authors.initials: P
authors.lastname: Vinuesa
authors.forename: Bruno
authors.initials: B
authors.lastname: Contreras-Moreira
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping; D030541:Databases, Genetic; D001330:Electronic Data Processing; D059646:Genome Size; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000295:instrumentation / Q000379:methods*; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D026801:Synteny