Duplication with transposition distance to the root for $q$-ary strings

We study the duplication with transposition distance between strings of length $n$ over a $q$-ary alphabet and their roots. In other words, we investigate the number of duplication operations of the form $x = (abcd) \to y = (abcbd)$, where $x$ and $y$ are strings and $a$, $b$, $c$ and $d$ are their substrings, needed to get a $q$-ary string of length $n$ starting from the set of strings without duplications. For exact duplication, we prove that the maximal distance between a string of length at most $n$ and its root has the asymptotic order $n/\log n$. For approximate duplication, where a $β$-fraction of symbols may be duplicated incorrectly, we show that the maximal distance has a sharp transition from the order $n/\log n$ to $\log n$ at $β=(q-1)/q$. The motivation for this problem comes from genomics, where such duplications represent a special kind of mutation and the distance between a given biological sequence and its root is the smallest number of transposition mutations required to generate the sequence.

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