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Sequence Reconstruction for the Single-Deletion Single-Substitution Channel
Journal article   Peer reviewed

Sequence Reconstruction for the Single-Deletion Single-Substitution Channel

Wentu Song, Kui Cai and Tony Q. S. Quek
IEEE journal on selected areas in information theory, Vol.6, pp.232-247
2025

Abstract

Codes Data mining deletion DNA data storage Error correction Genetic communication Hamming distances Memory reconstruction codes Redundancy Sequence reconstruction substitution Symbols
The central problem in sequence reconstruction is to find the minimum number of distinct channel outputs required to uniquely reconstruct the transmitted sequence. According to Levenshtein's work in 2001, this number is determined by the size of the maximum intersection between the error balls of any two distinct input sequences of the channel. In this work, we study the sequence reconstruction problem for the q-ary single-deletion single-substitution channel for any fixed integer q\geq 2 . First, we prove that if two q-ary sequences of length n have a Hamming distance d\geq 2 , then the intersection size of their error balls is upper bounded by 2qn-3q-2-\delta _{q,2} , where \delta _{i,j} is the Kronecker delta, and this bound is achievable. Next, we prove that if two q-ary sequences have a Hamming distance d\geq 3 and a Levenshtein distance d_{\text {L}}\geq 2 , then the intersection size of their error balls is upper bounded by 3q+11 , and we show that the gap between this bound and the tight bound is at most 2.

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