Bioinformatics Methods for Microbial Detection and Forensic Diagnostic Design

This chapter reviews bioinformatics techniques that are used for the detection and identificationof microbial samples, and for further analysis of sequence information derived from microbial organisms. It begins with an overview of laboratory techniques used to create the diagnostic and forensic data, and then describes methods for sequencing, assembling, and analyzing genomic data. Algorithms for large-scale genome alignment and comparison, followed by methods for modeling protein structure are considered. The goal of bioinformatics in microbial forensics and diagnostics is to support the rapid identification of microbial samples, at a variety of levels of resolution (family, species, strain, and isolate). Techniques to accomplish this are based upon accurate determination and comparison of genomic sequence of high quality, combined with detailed analysis of the sequence to determine gene composition, protein structure, and the functional organization of the mechanisms of transmission and virulence. 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.