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Nucleic Acids Research Advance Access published online on October 18, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm845
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© 2007
The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

OrthoDB: the hierarchical catalog of eukaryotic orthologs

Evgenia V. Kriventseva3, Nazim Rahman1, Octavio Espinosa1 and Evgeny M. Zdobnov1,2,4,*

1Department of Genetic Medicine and Development, University of Geneva Medical School, 2Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 3Department of Structural Biology and Bioinformatics, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland and 4Imperial College London, South Kensington Campus, SW7 2AZ London, UK

*To whom correspondence should be addressed. Tel: +41 22 379 59 73; Fax: +41 22 379 57 06; Email: evgeny.zdobnov{at}medecine.unige.ch

Received August 20, 2007. Revised September 24, 2007. Accepted September 25, 2007.

The concept of orthology is widely used to relate genes across different species using comparative genomics, and it provides the basis for inferring gene function. Here we present the web accessible OrthoDB database that catalogs groups of orthologous genes in a hierarchical manner, at each radiation of the species phylogeny, from more general groups to more fine-grained delineations between closely related species. We used a COG-like and Inparanoid-like ortholog delineation procedure on the basis of all-against-all Smith-Waterman sequence comparisons to analyze 58 eukaryotic genomes, focusing on vertebrates, insects and fungi to facilitate further comparative studies. The database is freely available at http://cegg.unige.ch/orthodb


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