title: A high-throughput pipeline for the design of real-time PCR signatures.
abstract: 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.
authors.affiliation: Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
authors.forename: Ravi
authors.initials: R
authors.lastname: Vijaya Satya
authors.forename: Kamal
authors.initials: K
authors.lastname: Kumar
authors.forename: Nela
authors.initials: N
authors.lastname: Zavaljevski
authors.forename: Jaques
authors.initials: J
authors.lastname: Reifman
mesh_terms: D001483:Base Sequence; D042726:Burkholderia mallei / Q000235:genetics; D016957:Burkholderia pseudomallei / Q000235:genetics; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D016680:Genome, Bacterial; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity; D013211:Staphylococcus aureus / Q000145:classification / Q000235:genetics*