Optimizing the codon usage of synthetic gene with QPSO algorithm

被引：46

作者：

Cai, Yujie ^{[1
]}

Sun, Jun ^{[2
]}

Wang, Jie ^{[2
]}

Ding, Yanrui ^{[2
]}

Tian, Na ^{[2
]}

Liao, Xiangru ^{[1
]}

Xu, Wenbo ^{[2
]}

机构：

[1] JiangNan Univ, Sch Biotechnol, Key Lab Ind Biotechnol, Wuxi 214122, Jiangsu, Peoples R China

[2] JiangNan Univ, Sch Informat Technol, Wuxi 214122, Jiangsu, Peoples R China

来源：

JOURNAL OF THEORETICAL BIOLOGY | 2008年 / 254卷 / 01期

关键词：

quantum-behaved particle swarm; optimization; synonymous codon; codon usage; synthetic gene;

D O I：

10.1016/j.jtbi.2008.05.010

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Molecular Biology makes it possible to express foreign genes in microorganism, plants and animals. To improve the heterologous expression, it is important that the codon usage of sequence be optimized to make it adaptive to host organism. In this paper, a novel method based on Quantum-behaved Particle Swarm Optimization (QPSO) algorithm is developed to optimize the codon usage of synthetic gene. Compared to the existing probability methods, QPSO is able to generate better results when DNA/RNA sequence length is less than 6 Kb which is the commonly used range. While the software or web service based on probability method may not exclude all defined restriction sites when there are many undesired sites in the sequence, our proposed method can remove the undesired site efficiently during the optimization process. (C) 2008 Elsevier Ltd. All rights reserved.

引用

页码：123 / 127

页数：5

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