Codon optimizer: a freeware tool for codon optimization
Codon optimizer: a freeware tool for codon optimization
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DOI：
10.1016/s1046-5928(03)00213-4
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发表时间：
2003-10-01
影响因子：
1.6
通讯作者：
Fuglsang, A
中科院分区：
文献类型：
--
作者：
Fuglsang, A
选择在迄今为止研究的所有生物体中的密码子使用的确定中起主要作用。在高表达基因中，使用一组狭窄的密码子，这些密码子对应于更丰富的tRNA种类。这最大限度地减少了翻译过程中tRNA耗尽的风险。事实上，基因中的密码子可能是真正的瓶颈，特别是在外源基因在宿主中表达的情况下，其中高度表达基因中密码子的使用与外源基因来源的物种中密码子的使用不相似。在这种情况下，已经表明，在引入的基因中替换稀有密码子可以显著提高产量。此外，稀有密码子的替换可能会减少错误掺入的机会，并保护蛋白质免于过早更新。在这里，宣布了一款软件，它可以根据宿主高度表达基因的知识计算任何基因的密码子优化序列。此外，它还计算了基因的密码子适应指数，并确定了优化序列的内部I t型限制性位点。该程序在Windows下运行，可作为免费软件在学术界使用。(C)2003年爱思唯尔公司All rights reserved.
Selection plays a major role in the determination of codon usage in all organisms studied so far. In highly expressed genes, a narrow set of codons is used and these codons correspond to the more abundant tRNA species. This minimizes the risk of tRNA depletion during translation. In fact, the codons in a gene may be true bottlenecks, especially in cases where foreign genes are expressed in a host in which the usage of codons in highly expressed genes does not resemble the usage of codons in the species from which the foreign gene originates. In such cases, it has been shown that substitution of rare codons in the introduced gene may increase the yield dramatically. In addition, replacement of rare codons might decrease the chance of misincorporation and protect the protein from premature turnover. Here, a piece of software is announced that calculates a codon-optimized sequence of any gene based on knowledge of highly expressed genes of a host. In addition, it calculates the codon adaptation index of the gene and identifies internal type It restriction sites of the optimized sequence. The program runs under Windows and is available as freeware for use in academia. (C) 2003 Elsevier Inc. All rights reserved.