On conflict free DNA codes

DOI10.1007/S12095-020-00459-7MaRDI QIDQ2040342zbMATH OpenOpenAlexFDO

Authors K. G. Benerjee, Sourav Deb, M. K. Gupta

Publication date 13 July 2021

Published in Cryptography and Communications (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1902.04419

zbMATH Keywords

homopolymersDNA codesreverse-complement constraint\textit{GC}-content constraintconflict free DNA stringshairpin like secondary structuresHamming constraintreverse constraint

Mathematics Subject Classification ID

Coding and information theory (compaction, compression, models of communication, encoding schemes, etc.) (aspects in computer science) (68P30) Bounds on codes (94B65) Other types of codes (94B60)

Abstract: DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a special constraint. Each codeword of the DNA code has a specific property that any two consecutive sub-strings of the DNA codeword will not be the same (a generalization of homo-polymers constraint). This is in addition to the usual constraints such as Hamming, reverse, reverse-complement and $GC$-content. We believe that the new constraint will help further in reducing the errors during reading and writing data into the synthetic DNA strings. We also present a construction (based on a variant of stochastic local search algorithm) to calculate the size of the DNA codes with all the above constraints, which improves the lower bounds from the existing literature, for some specific cases. Moreover, a recursive isometric map between binary vectors and DNA strings is proposed. Using the map and the well known binary codes we obtain few classes of DNA codes with all the constraints including the property that the constructed DNA codewords are free from the hairpin-like secondary structures.

Recommendations

• Linear constructions for DNA codes
• Linear and nonlinear constructions of DNA codes with Hamming distance \(d\), constant GC-content and a reverse-complement constraint
• Coding and Cryptography
• DNA codes based on additive self-dual codes over \(\mathrm{GF}(4)\)
• scientific article; zbMATH DE number 1568800

Cites work

• scientific article; zbMATH DE number 1024080 (Why is no real title available?)
• scientific article; zbMATH DE number 1953221 (Why is no real title available?)
• scientific article; zbMATH DE number 1568800 (Why is no real title available?)
• Codes for DNA Sequence Profiles
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Cited in

(5)

• Mutually uncorrelated codes for DNA storage
• Channel models and error correction codes for DNA information storage
• DNA codes from skew dihedral group ring
• On duplication-free codes for disjoint or equal-length errors
• Constructions and decoding of GC-balanced codes for edit errors

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Uses Software

• Mfold

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