In protein engineering, generation of mutagenesis libraries is a key step to study the functions of mutants. To generate mutants with a desired composition of amino acids (AAs), a codon consisting of a mixture of nucleotides is widely applied. Several computational methods have been proposed to calculate a codon nucleotide composition for generating a given amino acid profile based on mathematical optimization. However, these previous methods need to manually tune weights of amino acids in objective functions, which are time-consuming and, more importantly, lack publicly available software implementations. Here, we develop CodonAdjust, a software to adjust a codon nucleotide composition for mimicking a given amino acid profile. We propose different options of CodonAdjust, which provide various customizations in practical scenarios such as setting a guaranteeing threshold for the frequencies of amino acids without any manual tasks. We demonstrate the capability of CodonAdjust in the experiments on the complementarity-determining regions (CDRs) of antibodies and T-cell receptors (TCRs) as well as millions of amino acid profiles from Pfam. These results suggest that CodonAdjust is a productive software for codon design and may accelerate library generation. CodonAdjust is freely available at https://github.com/tiffany-nguyen/CodonAdjust. Paper edited by Dr. Jeffery Saven, Board Member for PEDS.

中文翻译：

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CodonAdjust：一种用于计算机设计具有特定氨基酸特征的诱变文库的软件。

在蛋白质工程中，诱变文库的产生是研究突变体功能的关键步骤。为了产生具有所需氨基酸（AA）组成的突变体，广泛使用了由核苷酸混合物组成的密码子。已经提出了几种计算方法以基于数学优化来计算用于产生给定氨基酸谱的密码子核苷酸组成。但是，这些先前的方法需要手动调整目标函数中氨基酸的权重，这很耗时，而且更重要的是缺少公开可用的软件实现。在这里，我们开发了CodonAdjust，这是一种用于调整密码子核苷酸组成以模仿给定氨基酸特征的软件。我们提出了CodonAdjust的不同选择，在实际情况下可以进行各种自定义，例如无需任何手动任务即可为氨基酸频率设置保证阈值。我们证明了在抗体和T细胞受体（TCR）的互补决定区（CDR）以及来自Pfam的数百万个氨基酸谱的实验中，CodonAdjust的功能。这些结果表明，CodonAdjust是用于密码子设计的高效软件，可以加速库的生成。CodonAdjust可从https://github.com/tiffany-nguyen/CodonAdjust免费获得。我们证明了在抗体和T细胞受体（TCR）的互补决定区（CDR）以及来自Pfam的数百万个氨基酸谱的实验中，CodonAdjust的功能。这些结果表明，CodonAdjust是用于密码子设计的高效软件，可以加速库的生成。CodonAdjust可从https://github.com/tiffany-nguyen/CodonAdjust免费获得。我们证明了在抗体和T细胞受体（TCR）的互补决定区（CDR）以及来自Pfam的数百万个氨基酸谱的实验中，CodonAdjust的功能。这些结果表明，CodonAdjust是用于密码子设计的高效软件，可以加速库的生成。CodonAdjust可从https://github.com/tiffany-nguyen/CodonAdjust免费获得。PEDS董事会成员Jeffery Saven博士编辑的论文。