Genome-scale design of PCR primers and long oligomers for DNA microarrays
Genome-scale design of PCR primers and long oligomers for DNA microarrays
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DOI：
10.1093/nar/gkg752
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发表时间：
2003-10-01
影响因子：
14.9
通讯作者：
Vingron, M
中科院分区：
文献类型：
--
作者：
Haas, SA;Hild, M;Vingron, M
近年来，对定制的cDNA芯片/阵列以及全基因组芯片的需求迅速增长。基因特异性引物/寡核苷酸的高效选择对于此类芯片的成功生产至关重要。我们开发了GenomePRIDE，这是一款高度灵活且可扩展的软件，用于为大规模项目设计引物/寡核苷酸。该程序能够生成长寡核苷酸（40 - 70个碱基），或者用于扩增用户定义长度的基因特异性DNA片段的PCR引物。此外，引物可以按读码框设计，以便于大规模克隆到表达载体中。而且，GenomePRIDE可适应特定应用，比如生成基因组扩增子阵列或设计针对可变剪接异构体的特异性片段。我们在单核细胞增生李斯特菌（1584个基因特异性PCR，48个长寡核苷酸）以及真核生物如粟酒裂殖酵母（5006个基因特异性PCR）和黑腹果蝇（21306个基因特异性PCR）的全基因组上测试了GenomePRIDE的性能。凭借每小时1000对引物的计算速度以及99%的PCR扩增成功率，GenomePRIDE是一款极具成本效益和时间效益的程序。
During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software for designing primers/oligomers for large-scale projects. The program is able to generate either long oligomers (40-70 bases), or PCR primers for the amplification of gene-specific DNA fragments of user-defined length. Additionally, primers can be designed in-frame in order to facilitate large-scale cloning into expression vectors. Furthermore, GenomePRIDE can be adapted to specific applications such as the generation of genomic amplicon arrays or the design of fragments specific for alternative splice isoforms. We tested the performance of GenomePRIDE on the entire genomes of Listeria monocytogenes (1584 gene-specific PCRs, 48 long oligomers) as well as of eukaryotes such as Schizosaccharomyces pombe (5006 gene-specific PCRs), and Drosophila melanogaster (21306 gene-specific PCRs). With its computing speed of 1000 primer pairs per hour and a PCR amplification success of 99%, GenomePRIDE represents an extremely cost- and time-effective program.