Quality assessment of gene repertoire annotations with OMArk
Open accessAbstract
In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life. OMArk assesses not only the completeness but also the consistency of the gene repertoire as a whole relative to closely related species and reports likely contamination events. Analysis of 1,805 UniProt Eukaryotic Reference Proteomes with OMArk demonstrated strong evidence of contamination in 73 proteomes and identified error propagation in avian gene annotation resulting from the use of a fragmented zebra finch proteome as a reference. This study illustrates the importance of comparing and prioritizing proteomes based on their quality measures.
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OMArk single-copy completeness and consistency metrics did not reveal any systematic bias between annotation sources or between miniature and nonminiature species.
“OMArk single-copy completeness and consistency metrics did not reveal any systematic bias between annotation sources or between miniature and nonminiature species (SI Appendix, Fig. S20).”
From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [94]
In Results > Assembly and annotation comparisons (page unavailable), the paper reports small differences between Ensembl and NCBI annotations and says they confirm that OMArk is slightly biased by the origin of its reference proteomes. The Discussion likewise cautions about this bias. The passages do not address miniature versus nonminiature species. (LLM, conf=0.87)
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PSAURON: a tool for assessing protein annotation across a broad range of species
Sommer, M. J., Zimin, A. V., & Salzberg, S. L. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae189 · Cited by 29 · see citing works
Sudasinghe, H., Matschiner, M., Britz, R., Conway, K. W., Tan, H. H., Salzburger, W., Peichel, C. L., & Rüber, L. (2026) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2614605123
- Authors
- Nevers, Y., Warwick Vesztrocy, A., Rossier, V., Train, C.-M., Altenhoff, A., Dessimoz, C., & Glover, N. M.
- Affiliations
- SIB Swiss Institute of Bioinformatics (CH)
- University of Lausanne (CH)
- Corresponding author
- Nevers, Yannis
- Venue
- Nature Biotechnology
- Published
- 2024-02-21
- Volume
- 43
- Issue
- 1
- Pages
- 124-133
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- PMC
- PMC11738984
- OpenAlex
- W4391997424
- Cited by
- 186
- References
- 2
- Citations by year
- 2026: 88 · 2025: 73 · 2024: 20 · 2023: 4 · 2012: 1
- FWCI
- 23.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Biotechnology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- SERVAL (Université de Lausanne) (submittedVersion, cc-by)
- IRIS (submittedVersion, cc-by)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- ETH Zürich Research Collection
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Swiss Institute of Bioinformatics
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Keywords
- annotation quality assessment, gene family comparison, contamination detection, alignment-free sequence comparison, error propagation, biodiversity genomics
- MeSH terms
- Animals, Software, Proteome, Genomics, Databases, Protein, Molecular Sequence Annotation
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