title: CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences.
abstract: 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.
authors.affiliation: a Department of Materials Science and Biotechnology , Graduate School of Science and Engineering, Ehime University , Bunkyo-cho 3, Matsuyama , Ehime , Japan.
authors.forename: Kazuyuki
authors.initials: K
authors.lastname: Takai
mesh_terms: D001483:Base Sequence; D003062:Codon; D004247:DNA / Q000138:chemical synthesis* / Q000235:genetics; D015870:Gene Expression; D005796:Genes; D016366:Open Reading Frames; D012984:Software
chemical_list: D003062:Codon; D004247:DNA
keywords: codon optimization; mRNA; spreadsheet