CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences

Gene synthesis is getting more important with the growing availability of low-cost commercial services. The coding sequences are often “optimized” as for the relative synonymous codon usage (RSCU) before synthesis, which is generally included in the commercial services. However, the codon optimization processes are different among different providers and are often hidden from the users. Here, the d'Hondt method, which is widely adopted as a method for determining the number of seats for each party in proportional-representation public elections, is applied to RSCU fitting. This allowed me to make a set of electronic spreadsheets for manual design of protein coding sequences for expression in Escherichia coli, with which users can see the process of codon optimization and can manually edit the codons after the automatic optimization. The spreadsheets may also be useful for molecular biology education

随着低成本商业化基因合成服务的日益普及，基因合成的重要性愈发凸显。在合成前，蛋白编码序列通常会依据相对同义密码子使用偏嗜性（relative synonymous codon usage, RSCU）进行“优化”，该优化流程通常已包含在商业化服务中。然而，不同服务商的密码子优化流程各不相同，且往往不对用户公开。本研究将比例代表制公共选举中广泛用于分配各政党席位的登特法（d'Hondt method）应用于RSCU拟合。借此，笔者开发了一套可手动设计大肠杆菌（Escherichia coli）表达蛋白编码序列的电子表格工具，用户可通过该工具直观了解密码子优化的完整流程，并可在自动优化完成后手动编辑密码子。此外，该电子表格工具亦可用于分子生物学教学工作。