2025/10/01 by Elias Dohmen, Margaux Aubel, Lars A. Eicholt +4 · 1 voice · 1 citation
Biochemistry, Genetics and Molecular Biology · #Genomics and Phylogenetic Studies #Genomics and Rare Diseases #Gene expression and cancer classification
paper · pdf · doi:10.1093/bioinformatics/btaf539
openalex publication_date 2025/10/01 · openalex created_date 2025/10/07 · openalex updated_date 2026/07/29
MOTIVATION: De novo genes emerge from previously non-coding regions of the genome, challenging the traditional view that new genes primarily arise through duplication and adaptation of existing ones. Characterized by their rapid evolution and their novel structural properties or functional roles, de novo genes represent a young area of research. Therefore, the field currently lacks established standards and methodologies, leading to inconsistent terminology and challenges in comparing and reproducing results. RESULTS: This work presents a standardized annotation format to document the methodology of de novo gene datasets in a reproducible way. We developed DeNoFo, a toolkit to provide easy access to this format that simplifies annotation of datasets and facilitates comparison across studies. Unifying the different protocols and methods in one standardized format, while providing integration into established file formats, such as fasta or gff, ensures comparability of studies and advances new insights in this rapidly evolving field. AVAILABILITY AND IMPLEMENTATION: DeNoFo is available through the official Python Package Index (PyPI) and at https://github.com/EDohmen/denofo. All tools have a graphical user interface and a command line interface. The toolkit is implemented in Python3, available for all major platforms and installable with pip and uv.