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. This pipeline consists of a pre-processing step, a post-processing step, and three different stages. TOPSI extends the Tool for Oligonucleotide Fingerprint Identification (TOFI) framework to design signatures for real-time PCR-based diagnostic assays.
Assists polymerase chain reaction (PCR) users in their PCR-related tasks. PCRdrive is an online platform that provides high quality ready to use qPCR assays for gene expression analysis quantitative PCR (qPCR). This application is equipped with several functions, components of an electronic lab notebook (ELN) as well as teamworking opportunities. It also contains an archive of public PCRs.
Provides high-throughput gene expression and genotyping analysis software. Sequence Detection System is an application that creates and saves analysis templates on a per detector basis for use with other plates. It can export the results or data, up to 50 plates at once, as well as a selection of results columns, using the batch export utility. This software was developed for use with the Applied Biosystems 7900HT Fast Real Time PCR System.