Fast computation of a string duplication history under no-breakpoint-reuse (extended abstract)

Abstract

In this paper, we provide an O(n log2 n log log n log* n) algorithm to compute a duplication history of a string under no-breakpoint-reuse condition. Our algorithm is an efficient implementation of earlier work by Zhang et al. (2009). The motivation of this problem stems from computational biology, in particular from analysis of complex gene clusters. The problem is also related to computing edit distance with block operations, but in our scenario the start of the history is not fixed, but chosen to minimize the distance measure. © 2011 Springer-Verlag.