Fast computation of a string duplication history under no-breakpoint-reuse

Authors:
Broňa Brejová;Gad M. Landau;Tomáš Vinař
Affiliations:
Faculty of Mathematics, Physics, and Informatics, Comenius University, Bratislava, Slovakia;Department of Computer Science, University of Haifa, Haifa, Israel;Faculty of Mathematics, Physics, and Informatics, Comenius University, Bratislava, Slovakia
Venue:
SPIRE'11 Proceedings of the 18th international conference on String processing and information retrieval
Year:
2011

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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-breakpointreuse 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.