Scientific article

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

Published inNucleic acids research, vol. 39, no. Database issue, p. D283-288
Publication date2011

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. Here, we present the updated OrthoDB catalog of eukaryotic orthologs delineated at each radiation of the species phylogeny in an explicitly hierarchical manner of over 100 species of vertebrates, arthropods and fungi (including the metazoa level). New database features include 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 is freely accessible from http://cegg.unige.ch/orthodb.

  • Animals
  • Arthropods/genetics
  • Databases, Genetic
  • Drosophila melanogaster/genetics
  • Evolution, Molecular
  • Fungi/genetics
  • Genes
  • Genomics
  • Mice
  • Molecular Sequence Annotation
  • Phylogeny
  • Protein Structure, Tertiary
  • Proteins/genetics
  • Saccharomyces cerevisiae/genetics
  • Sequence Homology, Amino Acid
  • Vertebrates/genetics
Citation (ISO format)
WATERHOUSE, Robert et al. OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011. In: Nucleic acids research, 2011, vol. 39, n° Database issue, p. D283–288. doi: 10.1093/nar/gkq930
Main files (1)
Article (Published version)
ISSN of the journal0305-1048

Technical informations

Creation10/14/2013 12:13:00 PM
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