Orthology Delineation

Orthology Delineation

The concept of homology drives speculation on a gene’s function in any given species when its biological roles in other species are characterized. With reference to a specific species radiation homologous relations define orthologs, i.e. descendants from a single gene of the ancestor. The large-scale delineation of gene genealogies is a challenging task, and the numerous approaches to the problem reflect the importance of the concept of orthology as a cornerstone for comparative studies. We have developed a classification procedure that delineates orthologs at each radiation of the species phylogeny in an explicitly hierarchical manner of over 100 species of vertebrates, arthropods and fungi. Our OrthoDB resource features functional annotations, and quantification of evolutionary divergence and relations among orthologous groups. The interface features extended phyletic profile querying and enhanced text-based searches. The ever-increasing sampling of sequenced eukaryotic genomes brings a clearer account of the majority of gene genealogies that will facilitate informed hypotheses of gene function in newly sequenced genomes. Furthermore, uniform analysis across lineages as different as vertebrates, arthropods and fungi with divergence levels varying from several to hundreds of millions of years will provide essential data for uncovering and quantifying long-term trends of gene evolution. OrthoDB: www.orthodb.org

OrthoDB Publications

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simão FA, Pozdnyakov IA, Ioannidis P, Zdobnov EM.
Nucleic Acids Res.
PMID: 25428351

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

Waterhouse RM, Tegenfeldt F, Li J, Zdobnov EM, Kriventseva EV.
Nucleic Acids Res.
PMID: 23180791

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.

Waterhouse RM, Zdobnov EM, Tegenfeldt F, Li J, Kriventseva EV.
Nucleic Acids Res.
PMID: 20972218

OrthoDB: the hierarchical catalog of eukaryotic orthologs

Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM
Nucleic Acids Res. 2008 Jan;36(Database issue):D271-5. Epub 2007 Oct 18
PMID: 17947323