PMC:4996382 / 8324-9832 JSONTXT

{"project":"2_test","denotations":[{"id":"27600214-21906634-69478338","span":{"begin":1497,"end":1499},"obj":"21906634"},{"id":"27600214-12527788-69478339","span":{"begin":1500,"end":1502},"obj":"12527788"},{"id":"27600214-22829736-69478340","span":{"begin":1503,"end":1505},"obj":"22829736"}],"text":"2.3. Virtual Hybridization\nVH software was used to calculate in silico genome fingerprints based on the complementarity between the probes and the genome. VH can also calculate and simulate various thermodynamic parameters such as Gibbs free energy (ΔG°), number of mismatches and melting temperature (Tm).\nWe have used the set of 13-mer sized probes in previous studies and found this probe size to be suitable for studying bacterial genomes (0.5–10 Mbp). The virtual hybridization reaction between the UFC-13 probes and the Bacillus anthracis genomes is first performed to identify possible sites of DNA duplex formation. Then, a computer simulation of the hybridization reaction between probes in the array and the target sequences (genomes) is conducted to predict the hybridization patterns that can be possibly obtained under the experimental conditions set. VH is carried out in two steps. The first step aims to finding the sites where DNA duplex formation (probe-target) might most likely occur. Such sites are identified by comparing the probes sequence with that of the target, with basis on their bases complementarity; these sites are labeled “potential hybridization sites”. In the second step, the free energy between the probe and the potential hybridization sites is calculated. VH accurately maps the position of each probe in the genome, identifying specific probes for each Bacillus anthracis strain, and yielding a signal or the formation of a spot when the duplex is formed [13,15,16].\n"}