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BMCBI
2008

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

13 years 3 months ago
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...
Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar,
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Ravi Vijaya Satya, Nela Zavaljevski, Kamal Kumar, Jaques Reifman
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