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Bioinformatics Advance Access published online on October 26, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl549
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received June 15, 2006
Revised October 18, 2006
Accepted October 21, 2006

Article

Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays

Waibhav Tembe 1, Nela Zavaljevski 1, Elizabeth Bode 2, Catherine Chase 2, Jeanne Geyer 2, Leonard Wasieloski 2, Gary Benson 3, and Jaques Reifman 1 *

1 Biotechnology HPC Software Applications Institute, US Army Medical Research and Materiel Command, Ft. Detrick, MD, USA
2 Diagnostic Systems Division, US Army Medical Research Institute of Infectious Diseases, Ft. Detrick, MD, USA
3 Department of Biology, Boston University, Boston, MA, USA; Department of Computer Science, Boston University, Boston, MA, USA

* To whom correspondence should be addressed.
Jaques Reifman, E-mail: jaques.reifman{at}us.army.mil


  Abstract

Motivation: 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 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.

Availability: The implemented algorithm is available upon request.

Associate Editor: John Quackenbush
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