OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.

Détails

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Etat: Public
Version: Final published version
Licence: Non spécifiée
ID Serval
serval:BIB_7EAD49D651C6
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Compte-rendu: analyse d'une oeuvre publiée.
Collection
Publications
Titre
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs.
Périodique
Nucleic Acids Research
Auteur(s)
Waterhouse R.M., Tegenfeldt F., Li J., Zdobnov E.M., Kriventseva E.V.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Statut éditorial
Publié
Date de publication
2013
Peer-reviewed
Oui
Volume
41
Numéro
Database issue
Pages
D358-65
Langue
anglais
Résumé
The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB-the hierarchical catalog of orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation of orthologs at varying resolution by explicitly referring to the hierarchy of species radiations, now also adopted by other resources. The current release provides comprehensive coverage of animals and fungi representing 252 eukaryotic species, and is now extended to prokaryotes with the inclusion of 1115 bacteria. Functional annotations of orthologous groups are provided through mapping to InterPro, GO, OMIM and model organism phenotypes, with cross-references to major resources including UniProt, NCBI and FlyBase. Uniquely, OrthoDB provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and now extended with exon-intron architectures, syntenic orthologs and parent-child trees. The interactive web interface allows navigation along the species phylogenies, complex queries with various identifiers, annotation keywords and phrases, as well as with gene copy-number profiles and sequence homology searches. With the explosive growth of available data, OrthoDB also provides mapping of newly sequenced genomes and transcriptomes to the current orthologous groups.
Mots-clé
Animals, Cluster Analysis, Databases, Genetic, Evolution, Molecular, Genes, Genes, Bacterial, Genes, Fungal, Humans, Internet, Mice, Molecular Sequence Annotation, Phenotype, Phylogeny, Synteny
Pubmed
Web of science
Open Access
Oui
Création de la notice
20/09/2017 10:05
Dernière modification de la notice
03/01/2020 18:10
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