Brona Brejova, Martin Kravec, Gad M. Landau, Tomas Vinar. Fast computation of a string duplication history under no-breakpoint-reuse. Philos Trans A Math Phys Eng Sci, 372(2016):20130133. 2014. Early version appeared at SPIRE 2011.
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In this paper, we provide an O(n log(2) n log log n log* n) algorithm to compute a duplication history of a string under no-breakpoint-reuse condition. 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.