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@@ -10,19 +10,21 @@ license: apache-2.0
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  pipeline_tag: token-classification
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  ---
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- ![image/png](https://cdn-uploads.huggingface.co/production/uploads/64c9888b3137cc529d0761c4/GqKutRwiGGif69Gjd8Df3.png)
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  **CodonTransformer** is the ultimate tool for codon optimization, transforming protein sequences into optimized DNA sequences specific for your target organisms. Whether you are a researcher or a practitioner in genetic engineering, CodonTransformer provides a comprehensive suite of features to facilitate your work. By leveraging the Transformer architecture and a user-friendly Jupyter notebook, it reduces the complexity of codon optimization, saving you time and effort.
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  ## Authors
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- 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>‡
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  <sup>1</sup> Vector Institute for Artificial Intelligence, Toronto ON, Canada
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  <sup>2</sup> University of Toronto Scarborough; Department of Biological Science; Scarborough ON, Canada
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  <sup>3</sup> Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006 Paris, France
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  \* These authors contributed equally to this work.
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- ‡ To whom correspondence should be addressed: **amir.pandi@cri-paris.org** <br>
 
 
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  ## Use Case
@@ -53,7 +55,7 @@ output = predict_dna_sequence(
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  organism=organism,
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  device=DEVICE,
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  tokenizer_object=tokenizer,
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- model_object=model,
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  attention_type="original_full",
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  )
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  print(format_model_output(output))
 
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  pipeline_tag: token-classification
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  ---
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+ ![image/png](https://github.com/Adibvafa/CodonTransformer/raw/main/src/banner_final.png)
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  **CodonTransformer** is the ultimate tool for codon optimization, transforming protein sequences into optimized DNA sequences specific for your target organisms. Whether you are a researcher or a practitioner in genetic engineering, CodonTransformer provides a comprehensive suite of features to facilitate your work. By leveraging the Transformer architecture and a user-friendly Jupyter notebook, it reduces the complexity of codon optimization, saving you time and effort.
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  ## Authors
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+ 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>‡
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  <sup>1</sup> Vector Institute for Artificial Intelligence, Toronto ON, Canada
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  <sup>2</sup> University of Toronto Scarborough; Department of Biological Science; Scarborough ON, Canada
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  <sup>3</sup> Université Paris Cité, INSERM U1284, Center for Research and Interdisciplinarity, F-75006 Paris, France
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  \* These authors contributed equally to this work.
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+ ‡ To whom correspondence should be addressed:
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+ guillaume.filion@utoronto.ca, ariel.lindner@inserm.fr, amir.pandi@cri-paris.org
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+ <br>
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  ## Use Case
 
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  organism=organism,
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  device=DEVICE,
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  tokenizer_object=tokenizer,
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+ model=model,
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  attention_type="original_full",
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  )
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  print(format_model_output(output))