Koressaar Triinu, Jõers Kai, Remm Maido
Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.
Bioinformatics. 2009 Jun 1;25(11):1349-55. doi: 10.1093/bioinformatics/btp241. Epub 2009 Apr 8.
The concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor.
We have developed a novel computational method that identifies species-specific repeats from microbial organisms and automatically designs species-specific PCR primers for these repeats. We tested the methodology on 30 randomly chosen microbial species and we demonstrate that species-specific repeats longer than 300 bp exist in all these genomes. We also used our methodology to design species-specific PCR primers for 86 repeats from five medically relevant microbial species. These PCR primers were tested experimentally. We demonstrate that using species-specific repeats as a PCR template region can increase the sensitivity of PCR in diagnostic tests.
A web version of the method called MultiMPrimer3 was implemented and is freely available at (http://bioinfo.ut.ee/multimprimer3/).
生物样本中病原体DNA的浓度通常非常低。因此，诊断测试的灵敏度始终是一个关键因素。
我们开发了一种新颖的计算方法，该方法可从微生物中识别物种特异性重复序列，并自动为这些重复序列设计物种特异性PCR引物。我们在30个随机选择的微生物物种上测试了该方法，结果表明所有这些基因组中都存在长度超过300 bp的物种特异性重复序列。我们还使用我们的方法为来自五个医学相关微生物物种的86个重复序列设计了物种特异性PCR引物。对这些PCR引物进行了实验测试。我们证明，使用物种特异性重复序列作为PCR模板区域可以提高诊断测试中PCR的灵敏度。
实现了该方法的网络版本，称为MultiMPrimer3，可在（http://bioinfo.ut.ee/multimprimer3/）上免费获取。
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