Single-Error Detection and Correction for Duplication and Substitution Channels

Yuanyuan Tang; Yonatan Yehezkeally; Moshe Schwartz; Farzad Farnoud

doi:10.1109/TIT.2020.3006228

Single-Error Detection and Correction for Duplication and Substitution Channels

Yuanyuan Tang, Yonatan Yehezkeally, Moshe Schwartz, Farzad Farnoud

Department of Electrical & Computer Engineering

Ben-Gurion University of the Negev

Research output: Contribution to journal › Article › peer-review

Abstract

Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in which the substitutions occur only within the duplicated substrings, and one in which the location of substitutions is unrestricted. Both error-detecting and error-correcting codes are constructed, which can handle correctly any number of tandem duplications of a fixed length k, and at most a single substitution occurring at any time during the mutation process.

Original language	American English
Article number	9130733
Pages (from-to)	6908-6919
Number of pages	12
Journal	IEEE Transactions on Information Theory
Volume	66
Issue number	11
DOIs	https://doi.org/10.1109/TIT.2020.3006228
State	Published - 1 Nov 2020

Keywords

DNA storage
error correction
error detection
string-duplication systems

All Science Journal Classification (ASJC) codes

Information Systems
Computer Science Applications
Library and Information Sciences

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10.1109/TIT.2020.3006228

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abstract = "Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in which the substitutions occur only within the duplicated substrings, and one in which the location of substitutions is unrestricted. Both error-detecting and error-correcting codes are constructed, which can handle correctly any number of tandem duplications of a fixed length k, and at most a single substitution occurring at any time during the mutation process.",

keywords = "DNA storage, error correction, error detection, string-duplication systems",

author = "Yuanyuan Tang and Yonatan Yehezkeally and Moshe Schwartz and Farzad Farnoud",

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AU - Schwartz, Moshe

AU - Farnoud, Farzad

PY - 2020/11/1

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N2 - Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in which the substitutions occur only within the duplicated substrings, and one in which the location of substitutions is unrestricted. Both error-detecting and error-correcting codes are constructed, which can handle correctly any number of tandem duplications of a fixed length k, and at most a single substitution occurring at any time during the mutation process.

AB - Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in which the substitutions occur only within the duplicated substrings, and one in which the location of substitutions is unrestricted. Both error-detecting and error-correcting codes are constructed, which can handle correctly any number of tandem duplications of a fixed length k, and at most a single substitution occurring at any time during the mutation process.

KW - DNA storage

KW - error correction

KW - error detection

KW - string-duplication systems

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JO - IEEE Transactions on Information Theory

JF - IEEE Transactions on Information Theory

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ER -

Single-Error Detection and Correction for Duplication and Substitution Channels

Abstract

Keywords

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