Method and theory of genome profiling (GP) developed for identification and classification of organisms

Details of the method and theory on the genome profiling (GP), which provides with the method for species identification and classification of organisms, are first described. GP consists of three major steps: i.e., random PCR, micro-temperature gradient gel electrophoresis (μTGGE), and extraction and processing of featuring points contained in genome profiles (results of the former step) generating species identification dots (spiddos). Methodological, physical and biological meanings of ‘random PCR’, ‘μTGGE’, ‘spiddos’, ‘genome distance (dG)’ and others introduced in this study are originally discussed. This paper gives a base for understanding the diversity of GP achievements performed for 30 years written in an alternative review on GP (i.e., to appear in Briefings in Functional Genomics (in process)), especially underscoring the importance of the spiddos parameter for calculating closeness of species and constructing genome database. Spiddos contains such a kind of information termed as SIOWS (sequence information obtained without sequencing), which is essentially unique and important for the GP technology, derived from the sequence-specific DNA melting phenomenon together with DNA melting theory. Succeedingly, one can understand why GP enables us to draw the sufficient amount of information without sequencing of genomic DNA. This also explains why identification/classification of species can be so readily and universally done by GP. It requires the perspective on the nature of spiddos. Since this paper first provides detailed procedures of GP and in-depth theoretical explanation of the GP-related phenomena, a wide range of scientists (Bacteriology, Infectious Disease Medicine, Epidemiology, Environmental Science, Biodiversity Science, Mutagen Research, Taxonomy, Bio-database Science, and others) can engage in applications of GP, which is difficult without sufficient understanding of the method and theory of GP.