OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.

Détails

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Etat: Public
Version: Final published version
Licence: Non spécifiée
ID Serval
serval:BIB_D6264A126D72
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Compte-rendu: analyse d'une oeuvre publiée.
Collection
Publications
Titre
OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.
Périodique
Nucleic Acids Research
Auteur(s)
Kriventseva E.V., Tegenfeldt F., Petty T.J., Waterhouse R.M., Simão F.A., Pozdnyakov I.A., Ioannidis P., Zdobnov E.M.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Statut éditorial
Publié
Date de publication
2015
Peer-reviewed
Oui
Volume
43
Numéro
Database issue
Pages
D250-6
Langue
anglais
Résumé
Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software).
Mots-clé
Algorithms, Animals, Data Curation, Databases, Genetic, Eukaryota/genetics, Evolution, Molecular, Genome, Microbial, Humans, Sequence Homology, Software
Pubmed
Web of science
Open Access
Oui
Création de la notice
20/09/2017 10:54
Dernière modification de la notice
03/01/2020 19:00
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