Fundamental Limits of Reference-Based Sequence Reordering

Nir Weinberger, Ilan Shomorony

Abstract: The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence is considered. First, in the regime in which the fragments are relatively long, and typically no fragment appears more than once, the scaling of the failure probability of maximum likelihood reconstruction algorithm is exactly determined for perfect reconstruction and bounded for partial reconstruction. Second, the regime in which the fragments are relatively short and repeating fragments abound is characterized. A trade-off is stated between the fraction of fragments that fail to be adequately reconstructed vs. the distortion level allowed for the reconstruction of each fragment, while still allowing vanishing failure probability.