2.5. Genomic Fingerprints
VH data were used to create a unique genomic fingerprint specific for each bacterial strain. UFA (Universal Fingerprint Analysis) generated an in silico microarray for each bacterium. The software output shows the number of columns and rows (spots) on the microarray.
Figure 2  Virtual hybridization (VH)—Extended method. Illustrative example of four probes used to predict sites where virtual hybridization with the target genome (represented by the blue line) might potentially occur. The VH software estimates the ΔG° value for each of the probes, adds four bases at the ends of the 13-nucleotide probes to yield 21-bases long (4 + 13 + 4) segments, and identifies whether the sequences are identical. It is statistically highly unlikely for two sequences of this length to have a high degree of similarity by chance.   The genomic fingerprint obtained shows the sites where virtual hybridization with the genome took place and identifies the positions where a DNA heteroduplex was formed. The fingerprint obtained can then be compared to other fingerprints to identify spots that are specific for individual bacteria. Visual microarrays render an image of the genomic fingerprint of each Bacillus anthracis. This image represents an in silico DNA microarray for a given organism, along with the specific probes used in hybridization experiments. This tool shows the set of 15,264 probes on a microarray as spots, color‑coded to identify those probes that hybridized with a particular target.
The microarray_pic software provides a very useful tool to display virtual hybridization patterns (fingerprint) graphically. This graphical representation shows the probes-to-target signals where a duplex was formed. Sites with high probability of virtual hybridization are shown with a green- or red-colored spot. Some probes can hybridize at multiple sites in the genome. In addition, two different tracks can be overlapped. The overlap shows, in yellow color, those probes that are shared by the two organisms; probes that are specific to one of the organisms are shown in green while those specific to the other organism are shown in red.
In silico genomic fingerprints were obtained for eight Bacillus anthracis strains. The fingerprints were obtained with the UFC-13 by virtual hybridization with 15,264 probes. Thermodynamic parameters used were: 1 mismatch and a ΔG° cutoff range of −19.53 to −11.67 kcal/mol. The method also identified those probes that are highly specific and highly potential for each Bacillus strain. The output file provides specific information for each microarray: (a) probe number; (b) probe ID; (c) position in the target sequence; (d) target sequence; and (e) ΔG°.