TmPrime: fast, flexible oligonucleotide design software for gene synthesis.
TmPrime: fast, flexible oligonucleotide design software for gene synthesis.
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DOI：
10.1093/nar/gkp461
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发表时间：
2009-07
影响因子：
14.9
通讯作者：
Ying JY
中科院分区：
文献类型：
--
作者：
Bode M;Khor S;Ye H;Li MH;Ying JY
在这里，我们提出了TmPrime，一个计算机程序来设计寡核苷酸集的基因组装连接酶链反应（LCR）和聚合酶链反应（PCR）。TmPrime提供了很大的灵活性，对基因和寡核苷酸长度没有限制。该程序基于输入的所需解链温度划分长输入DNA序列，并动态优化寡核苷酸的长度以实现同源解链温度。输出报告了解链温度、寡核苷酸序列和二级结构的潜在形成。我们的程序还提供了序列池功能，将长基因分离成较小的片段，用于多池组装和密码子优化表达。该软件已成功应用于绿色荧光蛋白片段（GFPuv）（760 bp）、人蛋白激酶B-2（PKB-2）（1446 bp）和人钙结合蛋白A4（S100 A4）启动子（752 bp）的实时PCR合成，为比较基因合成效率提供了一种新的方法。使用熔解曲线分析成功地估计了组装产物的纯度，这可能消除琼脂糖凝胶电泳的必要性。该程序可在http://prime.ibn.a-star.edu.sg上免费获得。
Herein we present TmPrime, a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). TmPrime offers much flexibility with no constraints on the gene and oligonucleotide lengths. The program divides the long input DNA sequence based on the input desired melting temperature, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences and potential formation of secondary structures. Our program also provides functions on sequence pooling to separate long genes into smaller pieces for multi-pool assembly and codon optimization for expression. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp) using real-time PCR assembly with LCGreen I, which offers a novel approach to compare the efficiency of gene synthesis. The purity of assembled products is successfully estimated with the use of melting curve analysis, which would potentially eliminate the necessity for agarose gel electrophoresis. This program is freely available at http://prime.ibn.a-star.edu.sg.
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影响因子：
6.1
作者：
Huang, Mo Chao;Ye, Hongye;Ying, Jackie Y.
通讯作者：
Ying, Jackie Y.
DOI：
10.1093/protein/5.8.827
发表时间：
1992-12-01
期刊：
PROTEIN ENGINEERING
影响因子：
--
作者：
PRODROMOU, C;PEARL, LH
通讯作者：
PEARL, LH
影响因子：
2.7
作者：
Hecker, KH;Rill, RL
通讯作者：
Rill, RL
影响因子：
14.9
作者：
Kong DS;Carr PA;Chen L;Zhang S;Jacobson JM
通讯作者：
Jacobson JM
影响因子：
14.9
作者：
Rydzanicz R;Zhao XS;Johnson PE
通讯作者：
Johnson PE