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OrthoDB v10: Sampling the Diversity of Animal, Plant, Fungal, Protist, Bacterial and Viral Genomes for Evolutionary and Functional Annotations of Orthologs

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OrthoDB v10: Sampling the Diversity of Animal, Plant, Fungal, Protist, Bacterial and Viral Genomes for Evolutionary and Functional Annotations of Orthologs

Evgenia V Kriventseva et al. Nucleic Acids Res.

Abstract

OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488 viruses. These include putative orthologs among 448 metazoan, 117 plant, 549 fungal, 148 protist, 5609 bacterial, and 404 archaeal genomes, picking up the best sequenced and annotated representatives for each species or operational taxonomic unit. OrthoDB relies on a concept of hierarchy of levels-of-orthology to enable more finely resolved gene orthologies for more closely related species. Since orthologs are the most likely candidates to retain functions of their ancestor gene, OrthoDB is aimed at narrowing down hypotheses about gene functions and enabling comparative evolutionary studies. Optional registered-user sessions allow on-line BUSCO assessments of gene set completeness and mapping of the uploaded data to OrthoDB to enable further interactive exploration of related annotations and generation of comparative charts. The accelerating expansion of genomics data continues to add valuable information, and OrthoDB strives to provide orthologs from the broadest coverage of species, as well as to extensively collate available functional annotations and to compute evolutionary annotations. The data can be browsed online, downloaded or assessed via REST API or SPARQL RDF compatible with both UniProt and Ensembl.

Figures

Figure 1.
Figure 1.
OrthoDB graphical abstract depicting the data processing pipeline.

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