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

SUBMITTER: Vijaya Satya R 

PROVIDER: S-EPMC2905370 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature