Competitive binding-based optical DNA mapping for fast identification of bacteria--multi-ligand transfer matrix theory and experimental applications on Escherichia coli.
Bottom Line: Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold.The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains.The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.Show MeSH
Related in: MedlinePlus
Mentions: We henceforth use P-values to quantify agreement between experiments and theory and use the phrase ‘reliable match’, for scenarios when the experiment-theory match is significantly better than what we would expect by chance, i.e. when P < Pthreshold. Using Pthreshold = 10% we find that 12 of the 36 fragments have a P-value that is below the threshold, although there is also a significant fraction with larger P's (see Figure 7A). By investigating the horizontal bars in Figure 6A, where IS and P-values are indicated, we note that fragments with P-values larger than 10% are typically short and have a small IS.
Affiliation: Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden.