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Interrogating nucleotide sequences with AI to understand codon usage patterns

The translation of messenger RNAs (mRNA) into proteins exemplifies the remarkable complexity of molecular biology that has been sculpted by evolution. The genetic code maps 61 codons (sequence of three… Click to show full abstract

The translation of messenger RNAs (mRNA) into proteins exemplifies the remarkable complexity of molecular biology that has been sculpted by evolution. The genetic code maps 61 codons (sequence of three nucleotides) to 20 amino acids, creating an expansive space of mRNA sequences that can code for protein sequences. Evolution, operating at the nucleotide level, has navigated this landscape to select for codon usage patterns that optimize for multiple factors such as mRNA stability ( 1 , 2 ), transfer RNA (tRNA) availability ( 3 ), transcription and translation efficiency ( 3 – 5 )

Keywords: interrogating nucleotide; nucleotide sequences; codon usage; sequences understand; usage patterns

Journal Title: Proceedings of the National Academy of Sciences of the United States of America
Year Published: 2025

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