On conflict free DNA codes

DOI10.1007/S12095-020-00459-7zbMATH Open1469.94171arXiv1902.04419OpenAlexW3093288951MaRDI QIDQ2040342FDOQ2040342

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

Publication date: 13 July 2021

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

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.

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

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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)

Cites Work

• Title not available (Why is that?)
• Linear constructions for DNA codes
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• Improved Lower Bounds for Constant GC-Content DNA Codes
• Linear and nonlinear constructions of DNA codes with Hamming distance \(d\) and constant \(GC\)-content
• Hairpin Structures in DNA Words
• Codes for DNA Sequence Profiles
• Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms

Cited In (3)

• Channel models and error correction codes for DNA information storage
• DNA codes from skew dihedral group ring
• Mutually uncorrelated codes for DNA storage

Uses Software

• Mfold

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