ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization.
ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization.
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DOI：
10.1186/s12859-015-0743-5
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发表时间：
2015-09-21
影响因子：
3
通讯作者：
Krause M
中科院分区：
文献类型：
--
作者：
Daniel E;Onwukwe GU;Wierenga RK;Quaggin SE;Vainio SJ;Krause M
当重组蛋白在不同生物体中表达时，密码子使用起着至关重要的作用。如果来源生物体和靶宿主生物体的密码子使用频率显著不同，例如当人基因在大肠杆菌中表达时，情况尤其如此。杆菌因此，为了能够或增强有效的基因表达，在任何给定的DNA序列中鉴定稀有密码子并随后将这些突变为在表达宿主中更频繁使用的密码子是非常重要的。我们描述了一个开源的基于网络的应用程序，ATGme，它可以在第一步确定罕见和高度罕见的密码子从大多数生物体，其次给用户优化序列的可能性。这个应用程序提供了一个简单的用户友好的界面，利用三个优化策略：1。一键优化，2.批量优化（通过密码子类型），3.个性化定制（逐个密码子）优化。ATGme是一个开源应用程序，可在以下网址免费获得：http://atgme.org
Codon usage plays a crucial role when recombinant proteins are expressed in different organisms. This is especially the case if the codon usage frequency of the organism of origin and the target host organism differ significantly, for example when a human gene is expressed in E. coli. Therefore, to enable or enhance efficient gene expression it is of great importance to identify rare codons in any given DNA sequence and subsequently mutate these to codons which are more frequently used in the expression host. We describe an open-source web-based application, ATGme, which can in a first step identify rare and highly rare codons from most organisms, and secondly gives the user the possibility to optimize the sequence. This application provides a simple user-friendly interface utilizing three optimization strategies: 1. one-click optimization, 2. bulk optimization (by codon-type), 3. individualized custom (codon-by-codon) optimization. ATGme is an open-source application which is freely available at: http://atgme.org