A high-throughput pipeline for designing microarray-based pathogen diagnostic assays

Background: We present a methodology for high-throughput design of oligonucleotide fingerprints for microarray-based pathogen diagnostic assays. The oligonucleotide fingerprints, or DNA microarray probes, are designed for identifying target organisms in environmental or clinical samples. The design process is implemented in a high-performance computing software pipeline that incorporates major algorithmic improvements over a previous version to both reduce computation time and improve specificity assessment. Results: The algorithmic improvements result in significant reduction in runtimes, with the updated pipeline being nearly up to five-times faster than the previous version. The improvements in specificity assessment, based on multiple specificity criteria, result in robust and consistent evaluation of cross-hybridization with nontarget sequences. In addition, the multiple criteria provide finer control on the number of resulting fingerprints, which helps in obtaining a larger numb...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Jaques Reifman
• Keywords: Algorithmic Improvements, BMCBI 2008, Oligonucleotide Fingerprints, Specificity Criteria