Shift-Interleave Coding for DNA-Based Storage: Correction of IDS Errors and Sequence Losses

We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs multiple codewords from two binary low-density parity-check codes....

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Bibliographic Details
Main Authors Shibata, Ryo, Kaneko, Haruhiko
Format Journal Article
LanguageEnglish
Published 25.01.2024
Subjects
Computer Science - Information Theory
Mathematics - Information Theory
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Summary:We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs multiple codewords from two binary low-density parity-check codes. These codewords are processed to form DNA base sequences through shifting, bit-to-base mapping, and interleaving. At the receiver side, an efficient non-iterative detection and decoding scheme is employed to sequentially estimate codewords. The numerical results demonstrate the excellent performance of the SI coding scheme in correcting both IDS errors and sequence losses.
DOI:10.48550/arxiv.2401.14594