The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity
Open accessAbstract
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.
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Cites
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OrthoFinder: phylogenetic orthology inference for comparative genomics
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Self-citationOrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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The InterPro protein families and domains database: 20 years on
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Ten Years of Collaborative Progress in the Quest for Orthologs
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Cited by
Gabriel, L., Brůna, T., Hoff, K. J., Ebel, M., Lomsadze, A., Borodovsky, M., & Stanke, M. (2024) · Genome Research · doi:10.1101/gr.278090.123 · Cited by 676
FlyBase: updates to the Drosophila genes and genomes database
Öztürk-Çolak, A., Marygold, S. J., Antonazzo, G., Attrill, H., Goutte-Gattat, D., Jenkins, V. K., Matthews, B. B., Millburn, G., dos Santos, G., Tabone, C. J., et al. (2024) · GENETICS · doi:10.1093/genetics/iyad211 · Cited by 412
(2023) · doi:10.1038/s41467-023-43702-4 · Cited by 55
Cosentino, S., Sriswasdi, S., & Iwasaki, W. (2024) · Genome Biology · doi:10.1186/s13059-024-03298-4 · Cited by 50
An episodic burst of massive genomic rearrangements and the origin of non-marine annelids
Vargas-Chávez, C., Benítez-Álvarez, L., Martínez-Redondo, G. I., Álvarez-González, L., Salces-Ortiz, J., Eleftheriadi, K., Escudero, N., Guiglielmoni, N., Flot, J.-F., Novo, M., et al. (2025) · Nature Ecology & Evolution · doi:10.1038/s41559-025-02728-1 · Cited by 35
Metadata
- Authors
- Kuznetsov, D., Tegenfeldt, F., Manni, M., Seppey, M., Berkeley, M., Kriventseva, E. V., & Zdobnov, E. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2022-11-09
- Volume
- 51
- Issue
- D1
- Pages
- D445-D451
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4308616062
- Cited by
- 522
- References
- 11
- FWCI
- 27.90
- Type
- journal article
- Language
- en
- Open access
- gold
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- Kuznetsov, D., Tegenfeldt, F., Manni, M., Seppey, M., Berkeley, M., Kriventseva, E. V., & Zdobnov, E. M. (2023). OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity. Nucleic Acids Research. https://doi.org/10.1093/nar/gkac998
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