OrthoDB in 2020: evolutionary and functional annotations of orthologs.

Animals Databases, Genetic Evolution, Molecular Molecular Sequence Annotation Sequence Homology, Nucleic Acid Software User-Computer Interface

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
08 01 2021
Historique:
accepted: 29 10 2020
revised: 12 10 2020
received: 15 09 2020
pubmed: 17 11 2020
medline: 27 1 2021
entrez: 16 11 2020
Statut: ppublish

Résumé

OrthoDB provides evolutionary and functional annotations of orthologs, inferred for a vast number of available organisms. OrthoDB is leading in the coverage and genomic diversity sampling of Eukaryotes, Prokaryotes and Viruses, and the sampling of Bacteria is further set to increase three-fold. The user interface has been enhanced in response to the massive growth in data. OrthoDB provides three views on the data: (i) a list of orthologous groups related to a user query, which are now arranged to visualize their hierarchical relations, (ii) a detailed view of an orthologous group, now featuring a Sankey diagram to facilitate navigation between the levels of orthology, from more finely-resolved to more general groups of orthologs, as well as an arrangement of orthologs into an interactive organism taxonomy structure, and (iii) we added a gene-centric view, showing the gene functional annotations and the pair-wise orthologs in example species. The OrthoDB standalone software for delineation of orthologs, Orthologer, is freely available. Online BUSCO assessments and mapping to OrthoDB of user-uploaded data enable interactive exploration of related annotations and generation of comparative charts. OrthoDB strives to predict orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations, and to compute evolutionary annotations such as evolutionary rate and phyletic profile. OrthoDB data can be assessed via SPARQL RDF, REST API, downloaded or browsed online from https://orthodb.org.

Identifiants

DOI: 10.1093/nar/gkaa1009 PMID: 33196836 PMC: PMC7779051
pubmed: 33196836
pii: 5983625
doi: 10.1093/nar/gkaa1009
pmc: PMC7779051
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

D389-D393

Informations de copyright

© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Evgeny M Zdobnov (EM)

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

Dmitry Kuznetsov (D)

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

Fredrik Tegenfeldt (F)

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

Mosè Manni (M)

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

Matthew Berkeley (M)

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

Evgenia V Kriventseva (EV)

Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland, and Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › OrthoDB in 2020: evolutionary and functional...
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › OrthoDB in 2020: evolutionary and functional...
questionsmedicales.fr › Phénomènes biologiques › Évolution biologique › Évolution moléculaire › OrthoDB in 2020: evolutionary and functional...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › OrthoDB in 2020: evolutionary and functional...
questionsmedicales.fr › Phénomènes génétiques › Similitude de séquences › Similitude de séquences d'acides nucléiques › OrthoDB in 2020: evolutionary and functional...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › OrthoDB in 2020: evolutionary and functional...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Interface utilisateur › OrthoDB in 2020: evolutionary and functional...