高通量实时 PCR 特征设计流水线。

A high-throughput pipeline for the design of real-time PCR signatures.

机构信息

Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.

出版信息

BMC Bioinformatics. 2010 Jun 23;11:340. doi: 10.1186/1471-2105-11-340.

BACKGROUND

Pathogen diagnostic assays based on polymerase chain reaction (PCR) technology provide high sensitivity and specificity. However, the design of these diagnostic assays is computationally intensive, requiring high-throughput methods to identify unique PCR signatures in the presence of an ever increasing availability of sequenced genomes.

RESULTS

We present the Tool for PCR Signature Identification (TOPSI), a high-performance computing pipeline for the design of PCR-based pathogen diagnostic assays. The TOPSI pipeline efficiently designs PCR signatures common to multiple bacterial genomes by obtaining the shared regions through pairwise alignments between the input genomes. TOPSI successfully designed PCR signatures common to 18 Staphylococcus aureus genomes in less than 14 hours using 98 cores on a high-performance computing system.

CONCLUSIONS

TOPSI is a computationally efficient, fully integrated tool for high-throughput design of PCR signatures common to multiple bacterial genomes. TOPSI is freely available for download at http://www.bhsai.org/downloads/topsi.tar.gz.

背景

基于聚合酶链反应（PCR）技术的病原体诊断检测具有高灵敏度和特异性。然而，这些诊断检测的设计计算量很大，需要高通量的方法来识别存在于不断增加的测序基因组中的独特 PCR 特征。

结果

我们提出了用于 PCR 特征识别的工具（Tool for PCR Signature Identification，TOPSI），这是一种用于设计基于 PCR 的病原体诊断检测的高性能计算管道。TOPSI 管道通过在输入基因组之间进行两两比对来获取共享区域，从而有效地设计了多个细菌基因组共有的 PCR 特征。使用高性能计算系统上的 98 个核，TOPSI 在不到 14 小时的时间内成功设计了 18 个金黄色葡萄球菌基因组共有的 PCR 特征。