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. 2023 Jan 6;51(D1):D445-D451.
doi: 10.1093/nar/gkac998.

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

Affiliations

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

Dmitry Kuznetsov et al. Nucleic Acids Res. .

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.

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Figures

Figure 1.
Figure 1.
Elements of OrthoDB web interface: (A) the ‘Advanced’ section of the web interface enables user-tailored selection of organisms to focus on, specifying explicitly relevant levels of orthology, or phyloprofile filters. (B) the OG-centric results page shows an interactive Sankey diagram facilitating the navigation between the levels-of-orthology, and it presents a bookmarklet link that one can drag & drop to the browser toolbar for easy OrthoDB queries next time with the same filter settings. (C) the gene-centric view provides available gene annotations and a list of pair-wise orthologs in example species. (D) One can search for species of interest to list pair-wise orthologs in this species.
Figure 2.
Figure 2.
Benchmark (https://lemortho.ezlab.org/refogs) of the OrthoLoger software on refOGs. (A) The distribution of the F1 metric over refOGs shows that for the majority of refOGs F1 > 80%. (B) Concordance on ‘Variation of Information’ between the methods and RefOGs. The lower values indicate more similar classifications.

References

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