Inferring hierarchical orthologous groups from orthologous gene pairs.

Hierarchical orthologous groups are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest. Identifying such groups is useful in a wide range of contexts, including inference of gene function, study of gene evolution dynamics and comparative g...

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Autores principales:	Adrian M Altenhoff, Manuel Gil, Gaston H Gonnet, Christophe Dessimoz
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/47e5a9cbb3914fdfb0dc816aff57b5d2
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id	oai:doaj.org-article:47e5a9cbb3914fdfb0dc816aff57b5d2
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spelling	oai:doaj.org-article:47e5a9cbb3914fdfb0dc816aff57b5d22021-11-18T08:01:36ZInferring hierarchical orthologous groups from orthologous gene pairs.1932-620310.1371/journal.pone.0053786https://doaj.org/article/47e5a9cbb3914fdfb0dc816aff57b5d22013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23342000/?tool=EBIhttps://doaj.org/toc/1932-6203Hierarchical orthologous groups are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest. Identifying such groups is useful in a wide range of contexts, including inference of gene function, study of gene evolution dynamics and comparative genomics. Hierarchical orthologous groups can be derived from reconciled gene/species trees but, this being a computationally costly procedure, many phylogenomic databases work on the basis of pairwise gene comparisons instead ("graph-based" approach). To our knowledge, there is only one published algorithm for graph-based hierarchical group inference, but both its theoretical justification and performance in practice are as of yet largely uncharacterised. We establish a formal correspondence between the orthology graph and hierarchical orthologous groups. Based on that, we devise GETHOGs ("Graph-based Efficient Technique for Hierarchical Orthologous Groups"), a novel algorithm to infer hierarchical groups directly from the orthology graph, thus without needing gene tree inference nor gene/species tree reconciliation. GETHOGs is shown to correctly reconstruct hierarchical orthologous groups when applied to perfect input, and several extensions with stringency parameters are provided to deal with imperfect input data. We demonstrate its competitiveness using both simulated and empirical data. GETHOGs is implemented as a part of the freely-available OMA standalone package (http://omabrowser.org/standalone). Furthermore, hierarchical groups inferred by GETHOGs ("OMA HOGs") on >1,000 genomes can be interactively queried via the OMA browser (http://omabrowser.org).Adrian M AltenhoffManuel GilGaston H GonnetChristophe DessimozPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 1, p e53786 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Adrian M Altenhoff Manuel Gil Gaston H Gonnet Christophe Dessimoz Inferring hierarchical orthologous groups from orthologous gene pairs.
description	Hierarchical orthologous groups are defined as sets of genes that have descended from a single common ancestor within a taxonomic range of interest. Identifying such groups is useful in a wide range of contexts, including inference of gene function, study of gene evolution dynamics and comparative genomics. Hierarchical orthologous groups can be derived from reconciled gene/species trees but, this being a computationally costly procedure, many phylogenomic databases work on the basis of pairwise gene comparisons instead ("graph-based" approach). To our knowledge, there is only one published algorithm for graph-based hierarchical group inference, but both its theoretical justification and performance in practice are as of yet largely uncharacterised. We establish a formal correspondence between the orthology graph and hierarchical orthologous groups. Based on that, we devise GETHOGs ("Graph-based Efficient Technique for Hierarchical Orthologous Groups"), a novel algorithm to infer hierarchical groups directly from the orthology graph, thus without needing gene tree inference nor gene/species tree reconciliation. GETHOGs is shown to correctly reconstruct hierarchical orthologous groups when applied to perfect input, and several extensions with stringency parameters are provided to deal with imperfect input data. We demonstrate its competitiveness using both simulated and empirical data. GETHOGs is implemented as a part of the freely-available OMA standalone package (http://omabrowser.org/standalone). Furthermore, hierarchical groups inferred by GETHOGs ("OMA HOGs") on >1,000 genomes can be interactively queried via the OMA browser (http://omabrowser.org).
format	article
author	Adrian M Altenhoff Manuel Gil Gaston H Gonnet Christophe Dessimoz
author_facet	Adrian M Altenhoff Manuel Gil Gaston H Gonnet Christophe Dessimoz
author_sort	Adrian M Altenhoff
title	Inferring hierarchical orthologous groups from orthologous gene pairs.
title_short	Inferring hierarchical orthologous groups from orthologous gene pairs.
title_full	Inferring hierarchical orthologous groups from orthologous gene pairs.
title_fullStr	Inferring hierarchical orthologous groups from orthologous gene pairs.
title_full_unstemmed	Inferring hierarchical orthologous groups from orthologous gene pairs.
title_sort	inferring hierarchical orthologous groups from orthologous gene pairs.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/47e5a9cbb3914fdfb0dc816aff57b5d2
work_keys_str_mv	AT adrianmaltenhoff inferringhierarchicalorthologousgroupsfromorthologousgenepairs AT manuelgil inferringhierarchicalorthologousgroupsfromorthologousgenepairs AT gastonhgonnet inferringhierarchicalorthologousgroupsfromorthologousgenepairs AT christophedessimoz inferringhierarchicalorthologousgroupsfromorthologousgenepairs
_version_	1718422599344586752

Inferring hierarchical orthologous groups from orthologous gene pairs.

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