000069428 001__ 69428
000069428 005__ 20180310132129.0
000069428 0247_ $$2doi$$a10.1128/AEM.02411-13
000069428 0248_ $$2sideral$$a84082
000069428 037__ $$aART-2013-84082
000069428 041__ $$aeng
000069428 100__ $$0(orcid)0000-0002-5462-907X$$aContreras-Moreira, B.
000069428 245__ $$aGET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis
000069428 260__ $$c2013
000069428 5060_ $$aAccess copy available to the general public$$fUnrestricted
000069428 5203_ $$aGET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles, or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain composition of proteins using the HMMER3 package, by imposing desired pairwise alignment coverage cutoffs, or by selecting only syntenic genes. The resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation, and graphical display of core genome and pangenome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core genome and pangenome sizes, and high-quality graphics can be generated. Furthermore, pangenome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50 Streptococcus genomes annotated in the Orthologous Matrix (OMA) browser as a benchmark case. The package can be downloaded at http://www.eead.csic.es/compbio/soft/gethoms.php and http://maya.ccg.unam.mx/soft/gethoms.php.
000069428 536__ $$9info:eu-repo/grantAgreement/ES/CSIC/ARAID/200720I038
000069428 540__ $$9info:eu-repo/semantics/openAccess$$aAll rights reserved$$uhttp://www.europeana.eu/rights/rr-f/
000069428 590__ $$a3.952$$b2013
000069428 591__ $$aMICROBIOLOGY$$b24 / 118 = 0.203$$c2013$$dQ1$$eT1
000069428 591__ $$aBIOTECHNOLOGY & APPLIED MICROBIOLOGY$$b30 / 161 = 0.186$$c2013$$dQ1$$eT1
000069428 655_4 $$ainfo:eu-repo/semantics/review$$vinfo:eu-repo/semantics/publishedVersion
000069428 700__ $$aVinuesa, P.
000069428 773__ $$g24, 7696-7701 (2013), 7696-7701$$pAppl. environ. microbiol.$$tAPPLIED AND ENVIRONMENTAL MICROBIOLOGY$$x0099-2240
000069428 8564_ $$s173522$$uhttps://zaguan.unizar.es/record/69428/files/texto_completo.pdf$$yVersión publicada
000069428 8564_ $$s135375$$uhttps://zaguan.unizar.es/record/69428/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000069428 909CO $$ooai:zaguan.unizar.es:69428$$particulos$$pdriver
000069428 951__ $$a2018-03-09-14:55:42
000069428 980__ $$aARTICLE