Example Files
This page provides downloadable example files from the DENOFO toolkit case studies, organized by species and study. Each file is accompanied by its corresponding reference for proper citation.
Fruit Fly (Drosophila melanogaster) Example Files
Study Annotation Files (DNGF Format)
Roginski et al. (2024)
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Grandchamp et al. (2023)
Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Research. 2023 Jun 1;33(6):872–90.
Zheng & Zhao (2022)
Zheng EB, Zhao L. Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins. eLife. 2022 Sep 30;11:e78772.
Pairwise Comparison Files (Similarities)
Roginski et al. (2024) vs Grandchamp et al. (2023)
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Research. 2023 Jun 1;33(6):872–90.
Fly_similarities_Roginski-2024_vs_Grandchamp-2023.txt
Zheng & Zhao (2022) vs Grandchamp et al. (2023)
Zheng EB, Zhao L. Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins. eLife. 2022 Sep 30;11:e78772.
Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Research. 2023 Jun 1;33(6):872–90.
Fly_similarities_Zheng-and-Zhao-2022_vs_Grandchamp-2023.txt
Zheng & Zhao (2022) vs Roginski et al. (2024)
Zheng EB, Zhao L. Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins. eLife. 2022 Sep 30;11:e78772.
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Pairwise Comparison Files (Differences)
Roginski et al. (2024) vs Grandchamp et al. (2023)
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Research. 2023 Jun 1;33(6):872–90.
Fly_differences_Roginski-2024_vs_Grandchamp-2023.txt
Zheng & Zhao (2022) vs Grandchamp et al. (2023)
Zheng EB, Zhao L. Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins. eLife. 2022 Sep 30;11:e78772.
Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Research. 2023 Jun 1;33(6):872–90.
Fly_differences_Zheng-and-Zhao-2022_vs_Grandchamp-2023.txt
Zheng & Zhao (2022) vs Roginski et al. (2024)
Zheng EB, Zhao L. Protein evidence of unannotated ORFs in Drosophila reveals diversity in the evolution and properties of young proteins. eLife. 2022 Sep 30;11:e78772.
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Human (Homo sapiens) Example Files
Study Annotation Files (DNGF Format)
Dowling et al. (2020)
Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic gain and loss of novel transcribed open reading frames in the human lineage. Genome Biology and Evolution. 2020 Nov;12(11):2183–95.
Roginski et al. (2024)
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Vakirlis et al. (2022)
Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Reports. 2022 Dec 20;41(12).
Pairwise Comparison Files (Similarities)
Dowling et al. (2020) vs Roginski et al. (2024)
Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic gain and loss of novel transcribed open reading frames in the human lineage. Genome Biology and Evolution. 2020 Nov;12(11):2183–95.
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Human_similarities_Dowling-2020_vs_Roginski-2024.txt
Vakirlis et al. (2022) vs Dowling et al. (2020)
Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Reports. 2022 Dec 20;41(12).
Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic gain and loss of novel transcribed open reading frames in the human lineage. Genome Biology and Evolution. 2020 Nov;12(11):2183–95.
Human_similarities_Vakirlis-2022_vs_Dowling-2020.txt
Vakirlis et al. (2022) vs Roginski et al. (2024)
Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Reports. 2022 Dec 20;41(12).
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Pairwise Comparison Files (Differences)
Dowling et al. (2020) vs Roginski et al. (2024)
Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic gain and loss of novel transcribed open reading frames in the human lineage. Genome Biology and Evolution. 2020 Nov;12(11):2183–95.
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Human_differences_Dowling-2020_vs_Roginski-2024.txt
Vakirlis et al. (2022) vs Dowling et al. (2020)
Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Reports. 2022 Dec 20;41(12).
Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic gain and loss of novel transcribed open reading frames in the human lineage. Genome Biology and Evolution. 2020 Nov;12(11):2183–95.
Human_differences_Vakirlis-2022_vs_Dowling-2020.txt
Vakirlis et al. (2022) vs Roginski et al. (2024)
Vakirlis N, Vance Z, Duggan KM, McLysaght A. De novo birth of functional microproteins in the human lineage. Cell Reports. 2022 Dec 20;41(12).
Roginski P, Grandchamp A, Quignot C, Lopes A. De Novo Emerged Gene Search in Eukaryotes with DENSE. Genome Biology and Evolution. 2024 Aug;16(8):evae159.
Additional Files
Annotated FASTA File (Dowling et al. 2020)
Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic gain and loss of novel transcribed open reading frames in the human lineage. Genome Biology and Evolution. 2020 Nov;12(11):2183–95.
Usage Notes
DNGF files: These are study annotation files in the De Novo Gene annotation Format, standardized for use with the DENOFO toolkit.
Similarities files: Output from the DENOFO comparator showing methodological similarities between studies.
Differences files: Output from the DENOFO comparator showing methodological differences between studies.
FASTA file: Contains annotated sequences from the corresponding study.
For more information about these files and their usage, please refer to the Case Studies, DENOFO Comparator, and Technical Documentation sections.