Rehbein Peter, Berz Jannik, Kreisel Patrick, Schwalbe Harald
Institute for Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Straße 35-37, 88400, Biberach, Germany.
Institute for Molecular Life Sciences, Department of Molecular Cell Biology of Plants, Goethe University Frankfurt, Max-von-Laue-Straße 7, 6043, Frankfurt Am Main, Germany.
Protein Expr Purif. 2019 Aug;160:84-93. doi: 10.1016/j.pep.2019.03.018. Epub 2019 Apr 4.
Optimization of coding sequences to maximize protein expression yield is often outsourced to external service providers during commercial gene synthesis and thus unfortunately remains a black box for many researchers. The presented software program "CodonWizard" offers scientists a powerful but easy-to-use tool for customizable codon optimization: The intuitive graphical user interface empowers even scientists inexperienced in the art to straightforward design, modify, test and save complex codon optimization strategies and to publicly share successful otimization strategies among the scientific community. "Codon Wizard" provides highly flexible features for sequence analysis and completely customizable modification/optimization of codon usage of any given input sequence data (DNA/RNA/peptide) using freely combinable algorithms, allowing for implementation of contemporary, well-established optimization strategies as well as novel, proprietary ones alike. Contrary to comparable tools, "Codon Wizard" thus finally opens up ways for an empirical approach to codon optimization and may also >be used completely offline to protect resulting intellectual property. As a benchmark, the reliability, intuitiveness and utility of the application could be demonstrated by increasing the yield of recombinant TEV-protease expressed in E. coli by several orders of magnitude after codon optimization using "CodonWizard" - Permanently available for download on the web at http://schwalbe.org.chemie.uni-frankfurt.de/node/3324.
在商业基因合成过程中，将编码序列优化以最大化蛋白质表达产量的工作通常外包给外部服务提供商，因此不幸的是，这对许多研究人员来说仍然是一个黑匣子。本文介绍的软件程序“密码子向导”为科学家提供了一个功能强大但易于使用的可定制密码子优化工具：直观的图形用户界面使即使是该领域经验不足的科学家也能直接设计、修改、测试和保存复杂的密码子优化策略，并在科学界公开分享成功的优化策略。“密码子向导”为序列分析提供了高度灵活的功能，并使用可自由组合的算法对任何给定的输入序列数据（DNA/RNA/肽）的密码子使用情况进行完全可定制的修改/优化，允许实施当代成熟的优化策略以及新颖的专有策略。与同类工具不同，“密码子向导”最终为密码子优化开辟了一条实证方法的途径，并且还可以完全离线使用以保护产生的知识产权。作为一个基准，使用“密码子向导”进行密码子优化后，在大肠杆菌中表达的重组烟草蚀纹病毒蛋白酶的产量提高了几个数量级，从而证明了该应用程序的可靠性、直观性和实用性——可在网页http://schwalbe.org.chemie.uni-frankfurt.de/node/3324上永久下载。
