OrthoDB: the hierarchical catalog of eukaryotic orthologs

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 radiatio...

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Bibliographic Details
Published in:Nucleic acids research 2008-01, Vol.36 (suppl-1), p.D271-D275
Main Authors: Kriventseva, Evgenia V, Rahman, Nazim, Espinosa, Octavio, Zdobnov, Evgeny M
Format: Article
Language:English
Subjects:
Animals
Databases, Genetic
Fungi - genetics
Genomics
Insecta - genetics
Internet
Phylogeny
Proteomics
User-Computer Interface
Vertebrates - genetics
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Summary: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
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkm845