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. 2011 Jan;39(Database issue):D289-94.
doi: 10.1093/nar/gkq1238. Epub 2010 Nov 27.

OMA 2011: orthology inference among 1000 complete genomes

Adrian M Altenhoff  1 , Adrian Schneider, Gaston H Gonnet, Christophe Dessimoz
Affiliations

OMA 2011: orthology inference among 1000 complete genomes

Adrian M Altenhoff et al. Nucleic Acids Res. 2011 Jan.

Abstract

OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the algorithmic pipeline--in particular regarding the treatment of alternative splicing, and new features of the web (OMA Browser) and programming interface (SOAP API). In the second part, we review the various representations provided by OMA and their typical applications. The database is publicly accessible at http://omabrowser.org.

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Figures

Figure 1.
Figure 1.
Growth of the OMA database since its first release.
Figure 2.
Figure 2.
Visualization of the 1000 genomes included in the 10th release of OMA. Lineage assignments are based on NCBI Taxonomy database (24). Note that the radial scale (mean number of genes/genome) is not cumulative, i.e. it refers to the height of individual “band sectors”.
Figure 3.
Figure 3.
The four types of ortholog grouping provided in OMA. (a) protein-centric view reports orthologs to a gene of reference; (b) genome pair view lists all orthologs between two species; (c) OMA group view displays sets of genes in which all pairs of genes are orthologs and (d) hierarchical groups, groups of genes that descend from a single common ancestral gene within a given taxonomic range.
See this image and copyright information in PMC

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