CodonTransformer: a multispecies codon optimizer using context-aware neural networks.

ABSTRACT: Degeneracy in the genetic code allows many possible DNA sequences to encode the same protein. Optimizing codon usage within a sequence to meet organism-specific preferences faces combinatorial explosion. Nevertheless, natural sequences optimized through evolution provide a rich source of data for machine learning algorithms to explore the underlying rules. Here, we introduce CodonTransformer, a multispecies deep learning model trained on over 1 million DNA-protein pairs from 164 organisms spanning all domains of life. The model demonstrates context-awareness thanks to its Transformers architecture and to our sequence representation strategy that combines organism, amino acid, and codon encodings. CodonTransformer generates host-specific DNA sequences with natural-like codon distribution pr

SUBMITTER: Fallahpour A 

PROVIDER: S-EPMC11968976 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature