| | --- |
| | license: |
| | - cc-by-4.0 |
| | size_categories: |
| | - 1M<n<10M |
| | tags: |
| | - DNA Sequences |
| | - Protein Sequences |
| | - Computational Biology |
| | - Bioinformatics |
| | - Synthetic Biology |
| | --- |
| | |
| |  |
| |
|
| |
|
| | # CodonTransformer Dataset |
| |
|
| | A comprehensive compilation of 1,001,197 DNA and protein sequence pairs, sourced from 164 organisms across Eukaryotes, Bacteria, and Archaea. |
| | This dataset provides a rich resource for various computational biology and bioinformatics applications such as studying gene sequences, codon usage, and protein expression across diverse species. |
| |
|
| | ## Dataset Contents |
| |
|
| | - 1,001,197 DNA-protein sequence pairs |
| | - Sequences from 164 organisms, including: |
| | - Eukaryotes: Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Mus musculus, Saccharomyces cerevisiae, Chlamydomonas reinhardtii, Nicotiana tabacum |
| | - Bacteria: Various Enterobacteriaceae species including Escherichia coli |
| | - Archaea: Thermococcus barophilus, Sulfolobus solfataricus |
| | - Chloroplast genomes: Chlamydomonas reinhardtii, Nicotiana tabacum |
| |
|
| | ## Data Collection and Preprocessing |
| |
|
| | - **Source**: NCBI resources |
| | - **Original Format**: Gene or CDS (Coding Sequence) |
| | - **Protein Sequences**: Translated using NCBI Codon Tables |
| | - **Quality Control**: |
| | - DNA sequences divisible by three in length |
| | - Start with a start codon |
| | - End with a single stop codon |
| |
|
| | ## Dataset Structure |
| |
|
| | Each entry contains: |
| | - DNA sequence |
| | - Corresponding protein sequence |
| | - Gene and organism information |
| |
|
| | ## Uses and Applications |
| |
|
| | This dataset is valuable for various research areas and applications, including: |
| | - Comparative genomics |
| | - Codon usage analysis |
| | - Protein expression optimization |
| | - Synthetic biology and genetic engineering |
| | - Machine learning models in bioinformatics |
| |
|
| | It has been used to train the CodonTransformer model for codon optimization tasks. |
| |
|
| | ## Authors |
| | Adibvafa Fallahpour<sup>1,2</sup>\*, Vincent Gureghian<sup>3</sup>\*, Guillaume J. Filion<sup>2</sup>‡, Ariel B. Lindner<sup>3</sup>‡, Amir Pandi<sup>3</sup>‡ |
| |
|
| | <sup>1</sup> Vector Institute for Artificial Intelligence, Toronto ON, Canada |
| | <sup>2</sup> University of Toronto Scarborough; Department of Biological Science; Scarborough ON, Canada |
| | <sup>3</sup> Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006 Paris, France |
| | \* These authors contributed equally to this work. |
| | ‡ To whom correspondence should be addressed: <br> |
| | guillaume.filion@utoronto.ca, ariel.lindner@inserm.fr, amir.pandi@cri-paris.org |
| | <br> |
| |
|
| | ## Additional Resources |
| | - **Project Website** <br> |
| | https://adibvafa.github.io/CodonTransformer/ |
| |
|
| | - **GitHub Repository** <br> |
| | https://github.com/Adibvafa/CodonTransformer |
| |
|
| | - **Google Colab Demo** <br> |
| | https://adibvafa.github.io/CodonTransformer/GoogleColab |
| |
|
| | - **PyPI Package** <br> |
| | https://pypi.org/project/CodonTransformer/ |
| |
|
| | - **Paper** <br> |
| | https://www.nature.com/articles/s41467-025-58588-7 |
| |
|
| |
|
| | ## Citation |
| | ``` |
| | @article{Fallahpour_Gureghian_Filion_Lindner_Pandi_2025, |
| | title={CodonTransformer: a multispecies codon optimizer using context-aware neural networks}, |
| | volume={16}, |
| | ISSN={2041-1723}, |
| | url={https://www.nature.com/articles/s41467-025-58588-7}, |
| | DOI={10.1038/s41467-025-58588-7}, |
| | number={1}, |
| | journal={Nature Communications}, |
| | author={Fallahpour, Adibvafa and Gureghian, Vincent and Filion, Guillaume J. and Lindner, Ariel B. and Pandi, Amir}, |
| | year={2025}, |
| | month=apr, |
| | pages={3205}, |
| | language={en} |
| | } |
| | ``` |
