Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays.
BACKGROUND
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.


RESULTS
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.


BACKGROUND
The implemented algorithm is available upon request.
Tembe
Waibhav
W
Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD Boston, MA, USA.
Zavaljevski
Nela
N
Bode
Elizabeth
E
Chase
Catherine
C
Geyer
Jeanne
J
Wasieloski
Leonard
L
Benson
Gary
G
Reifman
Jaques
J
D000465:Algorithms; D016172:DNA Fingerprinting / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis* / Q000145:classification*; D005604:Francisella tularensis / Q000145:classification / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010957:Plasmids / Q000235:genetics; D012984:Software; D012985:Software Design; D015010:Yersinia pestis / Q000145:classification / Q000235:genetics
D004269:DNA, Bacterial