title: A high-throughput pipeline for designing microarray-based pathogen diagnostic assays.
abstract: 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 number of fingerprints with high specificity. Simulation tests for Francisella tularensis and Yersinia pestis, using a well-established hybridization model to estimate cross-hybridization with nontarget sequences, show that the improved specificity criteria yield a larger number of fingerprints as compared to using a single specificity criterion.
  
  
  CONCLUSIONS
  The faster runtimes, achieved as the result of algorithmic improvements, are critical for extending the pipeline to process multiple target genomes. The larger numbers of identified fingerprints, obtained by considering broader specificity criteria, are essential for designing probes for hard-to-distinguish target sequences.
authors.affiliation: Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA. rvijaya@bioanalysis.org
authors.forename: Ravi
authors.initials: R
authors.lastname: Vijaya Satya
authors.forename: Nela
authors.initials: N
authors.lastname: Zavaljevski
authors.forename: Kamal
authors.initials: K
authors.lastname: Kumar
authors.forename: Jaques
authors.initials: J
authors.lastname: Reifman
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification*; D002874:Chromosome Mapping / Q000379:methods; D016172:DNA Fingerprinting / Q000379:methods*; D015342:DNA Probes / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D044404:Genomic Islands / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D015342:DNA Probes; D004269:DNA, Bacterial