| 起始密码子下游区域AT含量优化工具BestAT的开发与应用 |
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| 引用本文： | 余劲聪,唐龙盘,方柏山.起始密码子下游区域AT含量优化工具BestAT的开发与应用[J].生物信息学,2012,10(1):1-4. |
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| 作者姓名： | 余劲聪 唐龙盘 方柏山 |
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| 作者单位： | 1. 福建省高校工业生物技术重点实验室(华侨大学),福建厦门,361021
2. 福建省高校工业生物技术重点实验室(华侨大学),福建厦门,361021;厦门大学化学化工学院化学工程与生物工程系,福建厦门,361005 |
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| 基金项目： | 国家自然科学基金资助项目（21076172 30770059）; 高等学校博士学科点专项科研基金（20070385001）; 福建省高校产学合作科技重大项目（2010H6023） |
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| 摘 要： | 基因的表达水平受到起始密码子下游区域AT含量的影响,从巨大的序列集中筛选出具有特定AT含量和密码子用法特征的同义序列是一个繁琐的工作。本文研发AT含量优化工具"BestAT",初步解决了自动获取海量同义序列和充分展示同义序列的密码子用法特性两个关键问题,并且实现了与密码子用法数据库(CUD)的无缝结合,采用了密码子参数的原位标示和AT含量曲线等直观方式展示序列特性,为这类实验设计提供有力的支持。
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| 关 键 词： | 起始密码子下游区域 AT含量 密码子优化 BestAT软件 甘油脱氢酶 |
Development and application of BestAT tool for optimizing AT content of the initiation codon downstream region |
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| YU Jin-cong
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TANG Long-pan
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FANG Bai-shan.Development and application of BestAT tool for optimizing AT content of the initiation codon downstream region[J].China Journal of Bioinformation,2012,10(1):1-4. |
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| Authors: | YU Jin-cong TANG Long-pan FANG Bai-shan |
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| Institution: | 1.The Key Laboratory for Industrial Biotechnology of Fujian Higher Education(Huaqiao University),Xiamen 361021,China;2.Department of Chemical and Biochemical Engineering,College of Chemistry and Chemical Engineering,Xiamen University,Xiamen 361005,China) |
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| Abstract: | AT content of the initiation codon downstream region affects the expression level of a gene.Picking up synonymous sequences that have specific AT content and codon usage features from tremendous sequence set is a burdensome work.In this paper,the tool named BestAT for AT content optimization had been developed.The tool resolved two key issues,（i） auto-generating mass synonymous sequences and（ii） revealing their codon usage features in details.Moreover,the tool was closely incorporated to the Codon Usage Database（CUD）,and supported marking in situ codon parameters and showing visualized AT curve.All of those help to experimental design for AT content optimization powerfully. |
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| Keywords: | initiation codon downstream region AT content codon optimization BestAT software glycerol dehydrogenase |
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