We developed the OMArk software package for evaluating protein-coding gene annotation quality. In addition to assessing the completeness of a proteome, OMArk estimates the overall quality of the gene set’s content, a feature that will help to improve public protein sequence data.
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References
Blaxter, M. et al. Why sequence all eukaryotes? Proc. Natl Acad. Sci. USA 119, e2115636118 (2022). An article that presents the reasoning behind the ongoing massive sequencing of all eukaryotic genomes.
Salzberg, S. L. Next-generation genome annotation: we still struggle to get it right. Genome Biol. 20, 92 (2019). A piece summarizing the challenges of gene annotation.
Altenhoff, A. M. et al. OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA ecosystem. Nucleic Acids Res. https://doi.org/10.1093/nar/gkad1020 (2023). The latest paper presenting the OMA orthology database, which OMArk uses as reference.
Rossier, V., Vesztrocy, A. W., Robinson-Rechavi, M. & Dessimoz, C. OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. Bioinformatics https://doi.org/10.1093/bioinformatics/btab219 (2021). This paper describes OMAmer, the first step in the workflow of OMArk.
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This is a summary of: Nevers, Y. et al. Quality assessment of gene repertoire annotations with OMArk. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02147-w (2024).
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OMArk, a tool for gene annotation quality control, reveals erroneous gene inference. Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02155-w
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DOI: https://doi.org/10.1038/s41587-024-02155-w
