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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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf539","type":"journal-article","created":{"date-parts":[[2025,10,2]],"date-time":"2025-10-02T11:59:06Z","timestamp":1759406346000},"source":"Crossref","is-referenced-by-count":4,"title":["DeNoFo: a file format and toolkit for standardized, comparable <i>de novo<\/i> gene annotation"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7203-2314","authenticated-orcid":false,"given":"Elias","family":"Dohmen","sequence":"first","affiliation":[{"name":"Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1653-9441","authenticated-orcid":false,"given":"Margaux","family":"Aubel","sequence":"additional","affiliation":[{"name":"Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3985-3698","authenticated-orcid":false,"given":"Lars A","family":"Eicholt","sequence":"additional","affiliation":[{"name":"Institute for Evolution and Biodiversity, University of M\u00fcnster , M\u00fcnster 48151,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0297-723X","authenticated-orcid":false,"given":"Paul","family":"Roginski","sequence":"additional","affiliation":[{"name":"Institute for Integrative Biology of the Cell (I2BC), Universit\u00e9 Paris-Saclay, CEA, CNRS , Gif-sur-Yvette 91198,","place":["France"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0558-0983","authenticated-orcid":false,"given":"Victor","family":"Luria","sequence":"additional","affiliation":[{"name":"Department of Neuroscience, Yale School of Medicine , New Haven, CT 06510,","place":["United States"]},{"name":"Department of Systems Biology, Harvard Medical School , Boston, MA 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