On the duplication distance of binary strings
We study the tandem duplication distance between binary sequences and their roots. This distance is motivated by genomic tandem duplication mutations and counts the smallest number of tandem duplication events that are required to take one sequence to another. We consider both exact and approximate tandem duplications, the latter leading to a combined duplication/Hamming distance. The paper focuses on the maximum value of the duplication distance to the root. For exact duplication, denoting the maximum distance to the root of a sequence of length n by f(n), we prove that f(n) = Θ(n). For the case of approximate duplication, where a β-fraction of symbols may be duplicated incorrectly, we show using the Plotkin bound that the maximum distance has a sharp transition from linear to logarithmic in n at β = 1/2.
© 2016 IEEE. The authors would like to thank anonymous reviewers whose comments improved the presentation of this paper. This work was supported in part by the NSF Expeditions in Computing Program (The Molecular Programming Project), by a USA-Israeli BSF grant 2012/107, by an ISF grant 620/13, and by the Israeli I-Core program.