metadata

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^1,2*, Vincent Gureghian³*, Guillaume J. Filion²‡, Ariel B. Lindner³‡, Amir Pandi³‡

¹ Vector Institute for Artificial Intelligence, Toronto ON, Canada
² University of Toronto Scarborough; Department of Biological Science; Scarborough ON, Canada
³ 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:
[email protected], [email protected], [email protected]

Additional Resources

Project Website
https://adibvafa.github.io/CodonTransformer/
GitHub Repository
https://github.com/Adibvafa/CodonTransformer
Google Colab Demo
https://adibvafa.github.io/CodonTransformer/GoogleColab
PyPI Package
https://pypi.org/project/CodonTransformer/
Paper
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}
}