Gene composer: database software for protein construct design, codon engineering, and gene synthesis.
Gene composer: database software for protein construct design, codon engineering, and gene synthesis.
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DOI：
10.1186/1472-6750-9-36
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发表时间：
2009-04-21
影响因子：
3.5
通讯作者：
Stewart L
中科院分区：
文献类型：
--
作者：
Lorimer D;Raymond A;Walchli J;Mixon M;Barrow A;Wallace E;Grice R;Burgin A;Stewart L
为了提高高通量蛋白质结构测定的效率，我们开发了一个数据库软件包Gene Composer，它有助于蛋白质构建体及其密码子工程合成基因序列的信息丰富的设计。凭借其模块化工作流程设计和众多图形用户界面，Gene Composer使研究人员能够执行现代结构指导蛋白质工程和合成基因工程中使用的所有常见生物信息学步骤。交互式比对查看器允许研究人员同时可视化已知蛋白质二级结构、配体接触、水接触、晶体接触、B因子、溶剂可及区域、残基性质类型和其他几个有用的性质视图中的序列保守性。构建体设计模块使新型蛋白质构建体的设计变得容易，这些蛋白质构建体具有改变的N-和C-末端、内部插入或缺失、点突变和所需的亲和标签。这些修饰可以组合并排列成多个蛋白质构建体，然后通过计算机模拟虚拟克隆到定义的表达载体中。基因设计模块使用蛋白质-基因算法，该算法根据具有最小密码子使用阈值、定义的G：C%含量和通过同义密码子选择实现的期望序列特征的选择的密码子使用表，自动将蛋白质氨基酸序列反翻译成密码子工程化的核酸基因序列，所述同义密码子选择针对预期表达系统进行了优化。基因设计模块的基因到寡核苷酸算法规划出通过PCR合成所需基因构建体所需的所有重叠寡核苷酸和诱变引物，并通过最流行的亚克隆策略将其物理克隆到选定的载体中。我们提出了一个完整的描述基因作曲家的功能，和一个有效的基于PCR的合成基因组装程序与错配特异性核酸内切酶错误校正结合PIPE克隆。在一份姐妹手稿中，我们提供了关于基因合成器如何设计基因和蛋白质构建体的数据，这些数据可以提高蛋白质的产量，用于结构研究。
To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.
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影响因子：
64.8
作者：
Baek, Daehyun;Villen, Judit;Shin, Chanseok;Camargo, Fernando D.;Gygi, Steven P.;Bartel, David P.
通讯作者：
Bartel, David P.
影响因子：
3.5
作者：
Lin, YK;Cheng, G;Clark, TG
通讯作者：
Clark, TG
影响因子：
14.9
作者：
ASLANIDIS, C;DEJONG, PJ
通讯作者：
DEJONG, PJ
DOI：
10.1101/sqb.1969.034.01.082
发表时间：
1969-01-01
期刊：
COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY
影响因子：
--
作者：
MORSE, DE;MOSTELLER, RD;YANOFSKY, C
通讯作者：
YANOFSKY, C
影响因子：
2.9
作者：
Klock, Heath E.;Koesema, Eric J.;Lesley, Scott A.
通讯作者：
Lesley, Scott A.