Inferring hierarchical orthologous groups from orthologous gene pairs.
Inferring hierarchical orthologous groups from orthologous gene pairs.
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DOI：
10.1371/journal.pone.0053786
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Dessimoz C
中科院分区：
文献类型：
--
作者：
Altenhoff AM;Gil M;Gonnet GH;Dessimoz C
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).
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影响因子：
4.3
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
通讯作者：
Dessimoz, Christophe
DOI：
10.1007/978-1-61779-582-4_9
发表时间：
2012-01-01
期刊：
EVOLUTIONARY GENOMICS: STATISICAL AND COMPUTATIONAL METHODS, VOL 1
影响因子：
--
作者：
Altenhoff, Adrian M.;Dessimoz, Christophe
通讯作者：
Dessimoz, Christophe
DOI：
10.1093/bioinformatics/btq229
发表时间：
2010-06-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Kristensen DM;Kannan L;Coleman MK;Wolf YI;Sorokin A;Koonin EV;Mushegian A
通讯作者：
Mushegian A
影响因子：
2.5
作者：
Karger, DR;Stein, C
通讯作者：
Stein, C
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM