| --- |
| 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} |
| } |
| ``` |
