Figure 2

Overview of the Genome Profiling (GP) method. The entire GP process consists of three steps: (A) Random sampling of DNA fragments from genomic DNA (i.e., random PCR), (B) acquisition of sequence information without sequencing (i.e., μTGGE analysis), and (C) computer-aided conversion of raw data to genome-intrinsic parameters (spiddos). (A) In Random PCR, primers bind to various regions of genomic DNA with mismatch-containing structures under low stringency conditions, leading to the generation of a set of fragments. (B) In μTGGE, DNA fragments loaded at the top of a slab gel migrate downward with a characteristic curvature caused by the temperature gradient. The pre- spiddo point of a DNA fragment (i.e., initiation of the melting-derived transition from double-stranded to single-stranded DNA) is indicated by a red dot. (C) Pre-spiddo points (red dots) are indicated in images a and b for genomes a and b, respectively. Species identification dots (spiddos), shown in diagrams a' and b', are obtained by normalizing the coordinates of pre-spiddo points with respect to internal reference DNA fragments (white dots). Spiddos thus obtained are used to calculate pattern similarity score (PaSS) or genomic distance (d _G  = 1 - PaSS).