Article

Oligonucleotide Fingerprint Identification for Microarray-Based Pathogen Diagnostic Assays

Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD Boston, MA, USA.
Bioinformatics (Impact Factor: 4.62). 02/2007; 23(1):5-13. DOI: 10.1093/bioinformatics/btl549
Source: PubMed

ABSTRACT Advances in DNA microarray technology and computational methods have unlocked new opportunities to identify 'DNA fingerprints', i.e. oligonucleotide sequences that uniquely identify a specific genome. We present an integrated approach for the computational identification of DNA fingerprints for design of microarray-based pathogen diagnostic assays. We provide a quantifiable definition of a DNA fingerprint stated both from a computational as well as an experimental point of view, and the analytical proof that all in silico fingerprints satisfying the stated definition are found using our approach.
The presented computational approach is implemented in an integrated high-performance computing (HPC) software tool for oligonucleotide fingerprint identification termed TOFI. We employed TOFI to identify in silico DNA fingerprints for several bacteria and plasmid sequences, which were then experimentally evaluated as potential probes for microarray-based diagnostic assays. Results and analysis of approximately 150 in silico DNA fingerprints for Yersinia pestis and 250 fingerprints for Francisella tularensis are presented.
The implemented algorithm is available upon request.

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    • "The identification tool was originally built in Perl language for use with both high-performance computing (HPC) and/or personal computers. It included various versions: TOFI alpha was the first version of the program and it is a personal computer version (Tembe et al., 2007); TOFI beta that included several optimisations and significantly reduced the overall execution time of the pipeline (Vijaya Satya et al., 2008); and a final version that included the parallel implementation for HPC (Ravi Vijaya, 2009). EDNA modified TOFI's pipeline by eliminating the UNAFold stage that involved microarray probe selection based on melting temperatures, and two-state folding or hybridisation calculations. "
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