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OMArk, a instrument for gene annotation high quality management, reveals inaccurate gene inference

Research Briefing Published: 21 February 2024 Nature Biotechnology (2024)Cite this article 433 Accesses 2 Altmetric Metrics details Subjects 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

OMArk, a instrument for gene annotation high quality management, reveals inaccurate gene inference

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We developed the OMArk software program package deal for evaluating protein-coding gene annotation high quality. Along with assessing the completeness of a proteome, OMArk estimates the general high quality of the gene set’s content material, a characteristic that can assist to enhance public protein sequence information.

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Fig. 1: OMArk idea and output graph.

References

  1. Blaxter, M. et al. Why sequence all eukaryotes? Proc. Natl Acad. Sci. USA 119, e2115636118 (2022). An article that presents the reasoning behind the continued huge sequencing of all eukaryotic genomes.

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  2. Salzberg, S. L. Subsequent-generation genome annotation: we nonetheless battle to get it proper. Genome Biol. 20, 92 (2019). A chunk summarizing the challenges of gene annotation.

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  3. Altenhoff, A. M. et al. OMA orthology in 2024: improved prokaryote protection, ancestral and extant GO enrichment, a revamped synteny viewer and extra within the OMA ecosystem. Nucleic Acids Res. https://doi.org/10.1093/nar/gkad1020 (2023). The most recent paper presenting the OMA orthology database, which OMArk makes use of as reference.

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  4. Rossier, V., Vesztrocy, A. W., Robinson-Rechavi, M. & Dessimoz, C. OMAmer: tree-driven and alignment-free protein project to subfamilies outperforms closest sequence approaches. Bioinformatics https://doi.org/10.1093/bioinformatics/btab219 (2021). This paper describes OMAmer, step one within the workflow of OMArk.

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Writer’s be aware Springer Nature stays impartial with regard to jurisdictional claims in revealed maps and institutional affiliations.

It is a abstract of: Nevers, Y. et al. High quality evaluation of gene repertoire annotations with OMArk. Nat. Biotechnol. https://doi.org/10.1038/s41587-024-02147-w (2024).

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OMArk, a instrument for gene annotation high quality management, reveals inaccurate gene inference.
Nat Biotechnol (2024). https://doi.org/10.1038/s41587-024-02155-w

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