Abstract
BackgroundOMA is a project that aims to identify orthologs within publicly available, complete genomes. With 657 genomes analyzed to date, OMA is one of the largest projects of its kind.ResultsThe algorithm of OMA improves upon standard bidirectional best-hit approach in several respects: it uses evolutionary distances instead of scores, considers distance inference uncertainty, includes many-to-many orthologous relations, and accounts for differential gene losses. Herein, we describe in detail the algorithm for inference of orthology and provide the rationale for parameter selection through multiple tests.ConclusionOMA contains several novel improvement ideas for orthology inference and provides a unique dataset of large-scale orthology assignments.
Highlights
OMA is a project that aims to identify orthologs within publicly available, complete genomes
Homologs can be divided into several classes [1]: orthologs, which originate from a speciation event; paralogs, which originate from gene duplication; and xenologs, which originate from horizontal gene transfer
A substantial reduction occurs with the classification of stable pairs from candidate pairs and serves to reduce the complexity of the verification step
Summary
OMA is a project that aims to identify orthologs within publicly available, complete genomes. The classification of genes according to evolutionary relations is essential for many aspects of comparative and functional genomics. Two genes that share a common ancestor are defined as homologs, while genes that are similar in sequence without a common origin are termed analogs. Homologs can be divided into several classes [1]: orthologs, which originate from a speciation event; paralogs, which originate from gene duplication; and xenologs, which originate from horizontal gene transfer. Evolutionary relations can be defined with respect to a third gene. In-paralogs are genes that diverged by a duplication that occurred after a speciation event of reference. Outparalogs are paralogs that diverged before a particular speciation event of reference
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