|
--- |
|
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: **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> |
|
TBD |
