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Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications by Albert Y. Zomaya, Mourad Elloumi

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CHAPTER 7

ALGORITHMIC ISSUES IN DNA BARCODING PROBLEMS

Bhaskar DasGupta, Ming-Yang Kao, and Ion Mndoiu

7.1 INTRODUCTION

In the outbreak of an epidemic, possibly as a result of biological warfare, there is an urgent need to identify the pathogen or the family it belongs to as early as possible. Armed with the identity of the pathogen or its family, and with prior knowledge of how the pathogen typically is spread, decision makers efficiently can alert the general public and first responders on how best to stave-off the invasion. Recent advances in genomic technologies, including the availability of a whole genome sequence for numerous pathogens and the improved sensitivity of a second generation of microarray-based hybridization platforms, have opened the way for the development of highly reliable genomic-based pathogen detection systems. However, the development of such a detection system appropriate for use by first responders still raises several challenging design issues. In addition to portability and cost-effectiveness, widespread use of such systems requires rapid and reliable identification from minute amounts of genetic material of mutated or artificially engineered unknown pathogens. At the same time, these systems should provide comprehensive coverage of known or partially known pathogens, robustness of the detection algorithms against malicious adversaries, and built-in ...

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