BIC Codes: Bit Insertion-based Constrained Codes with Error Correction for DNA Storage

In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maxi...

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Vydané v:	IEEE transactions on emerging topics in computing Ročník 11; číslo 3; s. 1 - 15
Hlavní autori:	Park, Seong-Joon, Park, Hosung, Kwak, Hee-Youl, No, Jong-Seon
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	New York IEEE 01.07.2023 The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Predmet:	Algorithms Binary data Bit insertion technique Codes constrained coding Constraints Decoding DNA DNA storage Encoding Error analysis Error correcting codes Error correction Error correction codes GC-content Insertion low-density parity-check (LDPC) code maxmimum homopolymer run Parity check codes rate-compatible code
ISSN:	2168-6750, 2168-6750
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Abstract	In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maximum homopolymer run (i.e., run-length (RL)) constraint by inserting dummy bits. We show that the BIC codes nearly achieves the capacity in terms of information density while the simple structure of the BIC codes allows linear-time encoding and fast parallel decoding. Also, by combining a balancing technique with the BIC codes, we obtain the constrained coding algorithm to satisfy the GC-content constraint as well as the RL constraint. Next, for DNA storage channel with errors, we integrate the proposed constrained coding algorithm with a rate-compatible low-density parity-check (LDPC) code to correct errors and erasures. Specifically, we incorporate LDPC codes adopted in the 5G new radio standard because they have powerful error-correction capability and appealing features for the integration. Simulation results show that the proposed integrated coding algorithm outperforms existing coding algorithms in terms of information density and error correctability.
AbstractList	In this article, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maximum homopolymer run (i.e., run-length (RL)) constraint by inserting dummy bits. We show that the BIC codes nearly achieves the capacity in terms of information density while the simple structure of the BIC codes allows linear-time encoding and fast parallel decoding. Also, by combining a balancing technique with the BIC codes, we obtain the constrained coding algorithm to satisfy the GC-content constraint as well as the RL constraint. Next, for DNA storage channel with errors, we integrate the proposed constrained coding algorithm with a rate-compatible low-density parity-check (LDPC) code to correct errors and erasures. Specifically, we incorporate LDPC codes adopted in the 5 G new radio standard because they have powerful error-correction capability and appealing features for the integration. Simulation results show that the proposed integrated coding algorithm outperforms existing coding algorithms in terms of information density and error correctability. In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained code called bit insertion-based constrained (BIC) code. BIC codes convert a binary data sequence to multiple oligo sequences satisfying the maximum homopolymer run (i.e., run-length (RL)) constraint by inserting dummy bits. We show that the BIC codes nearly achieves the capacity in terms of information density while the simple structure of the BIC codes allows linear-time encoding and fast parallel decoding. Also, by combining a balancing technique with the BIC codes, we obtain the constrained coding algorithm to satisfy the GC-content constraint as well as the RL constraint. Next, for DNA storage channel with errors, we integrate the proposed constrained coding algorithm with a rate-compatible low-density parity-check (LDPC) code to correct errors and erasures. Specifically, we incorporate LDPC codes adopted in the 5G new radio standard because they have powerful error-correction capability and appealing features for the integration. Simulation results show that the proposed integrated coding algorithm outperforms existing coding algorithms in terms of information density and error correctability.
Author	Kwak, Hee-Youl Park, Hosung Park, Seong-Joon No, Jong-Seon
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Snippet	In this paper, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained... In this article, we propose a new coding algorithm for DNA storage over both error-free and error channels. For the error-free case, we propose a constrained...
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SubjectTerms	Algorithms Binary data Bit insertion technique Codes constrained coding Constraints Decoding DNA DNA storage Encoding Error analysis Error correcting codes Error correction Error correction codes GC-content Insertion low-density parity-check (LDPC) code maxmimum homopolymer run Parity check codes rate-compatible code
Title	BIC Codes: Bit Insertion-based Constrained Codes with Error Correction for DNA Storage
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