r-scan statistics of a Poisson process with events transformed by duplications, deletions, and displacements

A stochastic model of a dynamic marker array in which markers could disappear, duplicate, and move relative to its original position is constructed to reflect on the nature of long DNA sequences. The sequence changes of deletions, duplications, and displacements follow the stochastic rules: (i) the original distribution of the marker array {…, X −2, X −1, X 0, X 1, X 2, …} is a Poisson process on the real line; (ii) each marker is replicated l times; replication or loss of marker points occur independently; (iii) each replicated point is independently and randomly displaced by an amount Y relative to its original position, with the Y displacements sampled from a continuous density g(y). Limiting distributions for the maximal and minimal statistics of the r-scan lengths (collection of distances between r + 1 successive markers) for the l-shift model are derived with the aid of the Chen-Stein method and properties of Poisson processes.</jats:p

Poisson approximations for conditional r-scan lengths of multiple renewal processes and application to marker arrays in biomolecular sequences

This study is motivated by problems of molecular sequence comparison for multiple marker arrays with correlated distributions. In this paper, the model assumes two (or more) kinds of markers, say Markers A and B, distributed along the DNA sequence. The two primary conditions of interest are (i) many of Marker B (say ≥ m) occur, and (ii) few of Marker B (say ≤ l) occur. We title these the conditional r-scan models, and inquire on the extent to which Marker A clusters or is over-dispersed in regions satisfying condition (i) or (ii). Limiting distributions for the extremal r-scan statistics from the A array satisfying conditions (i) and (ii) are derived by extending the Chen-Stein Poisson approximation method.</jats:p