Models of local behavior of DNA electrophoresis peak parameters

Many base calling algorithms implicitly or explicitly rely on predictions o f local sequence parameters such as amplitude, peak time and peak width. Fo r example, an algorithm may search for the next peak about a predicted peak time formed by adding the mean peak separation to the last position measur ement. In this paper, covariance models are presented which characterize th e dependence of peak parameters on those of other peaks. Based on experimen tal measurements, the model features an exponential decay in peak time jitt er covariance with respect to base separation. Both peak amplitude and peak width are modelled as being uncorrelated with those of adjacent bases. In the model, linear expressions are given to describe the growth in peak time jitter and peak width as a function of base position while other parameter s, such as amplitude variance, are modeled by constants. Together, these re sults form a simple model which may be used in the derivation of new sequen cing algorithms or in simulations for the testing of such algorithms. We su ggest that the correlation of the peak times is related to the Kuhn length of the single-stranded DNA fragments.