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

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.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Burkholderia mallei / genetics
  • Burkholderia pseudomallei / genetics
  • Chromosome Mapping
  • Computational Biology / methods*
  • Genome, Bacterial*
  • Polymerase Chain Reaction / methods*
  • Sensitivity and Specificity
  • Staphylococcus aureus / classification
  • Staphylococcus aureus / genetics*