The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes
Open accessAbstract
OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes. We collect gene annotations, delineate hierarchical gene orthology and annotate the orthologous groups (OGs) with functional and evolutionary traits. OrthoDB is the leading resource for species diversity, striving to sample the most diverse and well-researched organisms with the highest quality genomic data. This update expands to include 5827 eukaryotic genomes. We have also added coding DNA sequences (CDSs) and gene loci coordinates. OrthoDB can be browsed, downloaded, or accessed using REST API, SPARQL/RDF and now also via API packages for Python and R Bioconductor. OrthoLoger (https://orthologer.ezlab.org), the tool used for inferring orthologs in OrthoDB, is now available as a Conda package and through BioContainers. ODB-mapper, a component of OrthoLoger, streamlines annotation of genes from newly sequenced genomes with OrthoDB evolutionary and functional descriptors. The benchmarking sets of universal single-copy orthologs (BUSCO), derived from OrthoDB, had correspondingly a major update. The BUSCO tool (https://busco.ezlab.org) has become a standard in genomics, uniquely capable of assessing both eukaryotic and prokaryotic species. It is applicable to gene sets, transcriptomes, genome assemblies and metagenomic bins.
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OrthoFinder: phylogenetic orthology inference for comparative genomics
Emms, D. M., & Kelly, S. (2019) · Genome Biology · doi:10.1186/s13059-019-1832-y · Cited by 7,676
UniProt: the Universal Protein Knowledgebase in 2023
The UniProt Consortium, Bateman, A., Martin, M.-J., Orchard, S., Magrane, M., Ahmad, S., Alpi, E., Bowler-Barnett, E. H., Britto, R., Bye-A-Jee, H., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1052 · Cited by 7,210
O'Leary, N. A., Wright, M. W., Brister, J. R., Ciufo, S., Haddad, D., McVeigh, R., Rajput, B., Robbertse, B., Smith-White, B., Ako-Adjei, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1189 · Cited by 6,357
Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187
Self-citationKEGG for taxonomy-based analysis of pathways and genomes
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M., & Ishiguro-Watanabe, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac963 · Cited by 5,833
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
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Functional and evolutionary implications of gene orthology
Gabaldón, T., & Koonin, E. V. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3456 · Cited by 643
Ten Years of Collaborative Progress in the Quest for Orthologs
Linard, B., Ebersberger, I., McGlynn, S. E., Glover, N., Mochizuki, T., Patricio, M., Lecompte, O., Nevers, Y., Thomas, P. D., Gabaldón, T., et al. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab098 · Cited by 45
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Malovichko, Y. V., Bein, B., Gonzales-Irribarren, A., Leushkin, E., Hilgers, L., Stephen, A., Yi, X., Albertini, M., Stadager, T., Zumpt, M., et al. (2026) · doi:10.64898/2026.06.30.735536 · Cited by 5
Madgaonkar, S. R., Chivukula, N., Garisetti, V., Marigoudar, S. R., Sharma, K. V., & Samal, A. (2026) · Environmental Toxicology and Chemistry · doi:10.1093/etojnl/vgag026
Metadata
- Authors
- Tegenfeldt, F., Kuznetsov, D., Manni, M., Berkeley, M., Zdobnov, E. M., & Kriventseva, E. V.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-11-13
- Volume
- 53
- Issue
- D1
- Pages
- D516-D522
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W4404328264
- Cited by
- 341
- References
- 10
- FWCI
- 39.62
- Type
- journal article
- Language
- en
- Open access
- gold
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