Scientific article
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English

OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

Published inNucleic acids research, vol. 51, no. D1, p. D445-D451
Publication date2023-01-06
First online date2022-11-09
Abstract

OrthoDB provides evolutionary and functional annotations of genes in a diverse sampling of eukaryotes, prokaryotes, and viruses. Genomics continues to accelerate our exploration of gene diversity and orthology is the most precise way of bridging gene functional knowledge with the rapidly expanding universe of genomic sequences. OrthoDB samples the most diverse organisms with the best quality genomics data to provide the leading coverage of species diversity. This update of the underlying data to over 18 000 prokaryotes and almost 2000 eukaryotes with over 100 million genes propels the coverage to another level. This achievement also demonstrates the scalability of the underlying OrthoLoger software for delineation of orthologs, freely available from https://orthologer.ezlab.org. In addition to the ab-initio computations of gene orthology used for the OrthoDB release, the OrthoLoger software allows mapping of novel gene sets to precomputed orthologs and thereby links to their annotations. The LEMMI-style benchmarking of OrthoLoger ensures its state-of-the-art performance and is available from https://lemortho.ezlab.org. The OrthoDB web interface has been further developed to include a pairwise orthology view from any gene to any other sampled species. OrthoDB-computed evolutionary annotations as well as extensively collated functional annotations can be accessed via REST API or SPARQL/RDF, downloaded or browsed online from https://www.orthodb.org.

Keywords
  • Biological Evolution
  • Databases, Genetic
  • Eukaryota / genetics
  • Evolution, Molecular
  • Genomics
  • Molecular Sequence Annotation
  • Software
Citation (ISO format)
KOUZNETSOV, Dimitri et al. OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. In: Nucleic acids research, 2023, vol. 51, n° D1, p. D445–D451. doi: 10.1093/nar/gkac998
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Journal ISSN0305-1048
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