PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens

Background: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-toorder probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. Results: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Sreedevi Thiyagarajan, Miloslav Karhanek, Michael Akhras, Ronald W. Davis, Nader Pourmand
• Keywords: BMCBI 2006, Detection, MIP Assay, Molecular Inversion Probes