Codes Correcting a Single Long Duplication Error

Abstract

We consider the problem of constructing a code capable of correcting a single long tandem duplication error of variable length. As the main contribution of this paper, we present a $q$-ary efficiently encodable code of length $n+1$ and redundancy $1$ that can correct a single duplication of length at least $K=4\cdot\lceil \log_q n\rceil +1$. The complexity of encoding is $O(\frac{n^2}{\log n})$ and the complexity of decoding is $O(n)$. We also present a $q$-ary non-efficient code of length $n+1$ correcting single long duplication of length at least $K = \lceil \log_q n\rceil +\phi(n)$, where $\phi(n)\rightarrow{\infty}$ as $n\rightarrow{\infty}$. This code has redundancy less than $1$ for sufficiently large $n$. Moreover, we show that in the class of codes correcting a single long duplication with redundancy $1$, the value $K$ in our constructions is order-optimal.