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Nucleic Acids Res. 2008 Jan;36(Database issue):D271-5. Epub 2007 Oct 18.

OrthoDB: the hierarchical catalog of eukaryotic orthologs.

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  • 1Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 rue Michel-Servet, Geneva, Switzerland.

Abstract

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.

PMID:
17947323
[PubMed - indexed for MEDLINE]
PMCID:
PMC2238902
Free PMC Article

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