Load model and tokenizer

tokenizer = AutoTokenizer.from_pretrained("adibvafa/CodonTransformer") model = BigBirdForMaskedLM.from_pretrained("adibvafa/CodonTransformer").to(device)

Set your input data

protein = "MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG" organism = "Escherichia coli general"

Predict with CodonTransformer

output = predict_dna_sequence( protein=protein, organism=organism, device=device, tokenizer=tokenizer, model=model, attention_type="original_full", deterministic=True ) print(format_model_output(output))

The output is:
<br>


```python
-----------------------------
|          Organism         |
-----------------------------
Escherichia coli general

-----------------------------
|       Input Protein       |
-----------------------------
MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG

-----------------------------
|      Processed Input      |
-----------------------------
M_UNK A_UNK L_UNK W_UNK M_UNK R_UNK L_UNK L_UNK P_UNK L_UNK L_UNK A_UNK L_UNK L_UNK A_UNK L_UNK W_UNK G_UNK P_UNK D_UNK P_UNK A_UNK A_UNK A_UNK F_UNK V_UNK N_UNK Q_UNK H_UNK L_UNK C_UNK G_UNK S_UNK H_UNK L_UNK V_UNK E_UNK A_UNK L_UNK Y_UNK L_UNK V_UNK C_UNK G_UNK E_UNK R_UNK G_UNK F_UNK F_UNK Y_UNK T_UNK P_UNK K_UNK T_UNK R_UNK R_UNK E_UNK A_UNK E_UNK D_UNK L_UNK Q_UNK V_UNK G_UNK Q_UNK V_UNK E_UNK L_UNK G_UNK G_UNK __UNK

-----------------------------
|       Predicted DNA       |
-----------------------------
ATGGCTTTATGGATGCGTCTGCTGCCGCTGCTGGCGCTGCTGGCGCTGTGGGGCCCGGACCCGGCGGCGGCGTTTGTGAATCAGCACCTGTGCGGCAGCCACCTGGTGGAAGCGCTGTATCTGGTGTGCGGTGAGCGCGGCTTCTTCTACACGCCCAAAACCCGCCGCGAAGCGGAAGATCTGCAGGTGGGCCAGGTGGAGCTGGGCGGCTAA

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}
}