The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.

Détails

Ressource 1Télécharger: gkx1019.pdf (3896.98 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_FC0F04688D1D
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces.
Périodique
Nucleic acids research
Auteur(s)
Altenhoff A.M., Glover N.M., Train C.M., Kaleb K., Warwick Vesztrocy A., Dylus D., de Farias T.M., Zile K., Stevenson C., Long J., Redestig H., Gonnet G.H., Dessimoz C.
ISSN
1362-4962 (Electronic)
ISSN-L
0305-1048
Statut éditorial
Publié
Date de publication
04/01/2018
Peer-reviewed
Oui
Volume
46
Numéro
D1
Pages
D477-D485
Langue
anglais
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Résumé
The Orthologous Matrix (OMA) is a leading resource to relate genes across many species from all of life. In this update paper, we review the recent algorithmic improvements in the OMA pipeline, describe increases in species coverage (particularly in plants and early-branching eukaryotes) and introduce several new features in the OMA web browser. Notable improvements include: (i) a scalable, interactive viewer for hierarchical orthologous groups; (ii) protein domain annotations and domain-based links between orthologous groups; (iii) functionality to retrieve phylogenetic marker genes for a subset of species of interest; (iv) a new synteny dot plot viewer; and (v) an overhaul of the programmatic access (REST API and semantic web), which will facilitate incorporation of OMA analyses in computational pipelines and integration with other bioinformatic resources. OMA can be freely accessed at https://omabrowser.org.
Mots-clé
Algorithms, Animals, Archaea/classification, Archaea/genetics, Archaea/metabolism, Bacteria/classification, Bacteria/genetics, Bacteria/metabolism, Biological Evolution, Computational Biology/methods, Databases, Genetic, Fungi/classification, Fungi/genetics, Fungi/metabolism, Gene Ontology, Genome, Humans, Internet, Molecular Sequence Annotation, Phylogeny, Plants/classification, Plants/genetics, Plants/metabolism, Protein Domains, Proteins/chemistry, Proteins/genetics, Proteins/metabolism, Synteny, Web Browser
Pubmed
Web of science
Open Access
Oui
Création de la notice
15/11/2017 11:25
Dernière modification de la notice
20/08/2019 17:27
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