Deep learning-based codon optimization with large-scale synonymous variant datasets enables generalized tunable protein expression

Abstract

A method includes generating one or more DNA sequences using a machine learning model using coding sequences; comparing the DNA sequences to one or more natural DNA sequences; and determining a codon naturalness. A computing system includes a processor; and a memory having stored thereon computer-executable instructions that, when executed by the one or more processors, cause the computing system to: generate one or more DNA sequences using a machine learning model using coding sequences; compare the DNA sequences to one or more natural DNA sequences; and determine a codon naturalness. A non-transitory computer-readable medium has stored thereon instructions that, when executed by one or more processors, cause a computer to: generate one or more DNA sequences using a machine learning model using coding sequences; compare the DNA sequences to one or more natural DNA sequences; and determine a codon naturalness.

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