OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.

Details

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State: Serval
Version: Final published version
Serval ID
serval:BIB_8A7FE1FBE3CE
Type
Article: article from journal or magazin.
Collection
Publications
Title
OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011.
Journal
Nucleic Acids Research
Author(s)
Waterhouse R.M., Zdobnov E.M., Tegenfeldt F., Li J., Kriventseva E.V.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Publication state
Published
Issued date
2011
Peer-reviewed
Oui
Volume
39
Number
Database issue
Pages
D283-8
Language
english
Abstract
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.

Keywords
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
Pubmed
Web of science
Open Access
Yes
Create date
20/09/2017 11:10
Last modification date
08/05/2019 21:39
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