Bioinformatics Methods for Microbial Detection and Forensic Diagnostic Design

Tom r. Slezak

Lawrence Livermore National Laboratory, Livermore, California

Steven l. Salzberg

Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland; The Institute for Genomic Research, Rockville, Maryland

This chapter reviews bioinformatics techniques that can be used for detection and identification of microbial samples, and for further analysis of sequence information derived from microbial organisms. We begin with an overview of laboratory techniques used to create the diagnostic and forensic data, and then describe methods for sequencing, assembling, and analyzing genomic data. We then consider algorithms for large-scale genome alignment and comparison, followed by methods for modeling protein structure. The chapter concludes with real-life examples demonstrating working systems for detection and analysis of the microbial pathogens, using both DNA and protein detection methods.

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