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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Bibliographic Details
Published in:IEEE transactions on emerging topics in computing Vol. 11; no. 3; pp. 1 - 15
Main Authors: Park, Seong-Joon, Park, Hosung, Kwak, Hee-Youl, No, Jong-Seon
Format: Journal Article
Language:English
Published: New York IEEE 01.07.2023
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subjects:
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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Summary: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.
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ISSN:2168-6750
2168-6750
DOI:10.1109/TETC.2023.3268274