Greedy construction of DNA codes and new bounds

DOI10.1007/S00200-019-00386-YMaRDI QIDQ2002146zbMATH OpenOpenAlexWikidataFDO

Authors Nabil Bennenni, T. Aaron Gulliver, Kenza Guenda

Publication date 11 July 2019

Published in Applicable Algebra in Engineering, Communication and Computing (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1505.06262

zbMATH Keywords

\textit{GC}-contentDNA codesedit distanceupper and lower bounds

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Linear codes (general theory) (94B05)

Abstract: In this paper, we construct linear codes over $mathbb{Z}_4$ with bounded $GC$-content. The codes are obtained using a greedy algorithm over $mathbb{Z}_4$. Further, upper and lower bounds are derived for the maximum size of DNA codes of length $n$ with constant $GC$-content $w$ and edit distance $d$.

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Cites work

• Bounds for DNA codes with constant GC-content
• Codes for DNA Sequence Profiles
• Coding and Cryptography
• Construction of constant GC-content DNA codes via a variable neighbourhood search algorithm
• Deterministic polynomial-time algorithms for designing short DNA words
• scientific article; zbMATH DE number 1568800 (Why is no real title available?)
• Improved Lower Bounds for Constant GC-Content DNA Codes
• Lexicodes over rings
• Linear and nonlinear constructions of DNA codes with Hamming distance \(d\) and constant \(GC\)-content
• Linear and nonlinear constructions of DNA codes with Hamming distance \(d\), constant GC-content and a reverse-complement constraint
• Linear constructions for DNA codes

Cited in

(9)

• Construction of constant GC-content DNA codes via a variable neighbourhood search algorithm
• Bounds for DNA codes with constant GC-content
• A genetic algorithm using triplet nucleotide encoding and DNA reproduction operations for unconstrained optimization problems
• Improved Lower Bounds for Constant GC-Content DNA Codes
• A Geometric Approach to Gibbs Energy Landscapes and Optimal DNA Codeword Design
• Linear and nonlinear constructions of DNA codes with Hamming distance \(d\) and constant \(GC\)-content
• DNA Computing
• Constructions and decoding of GC-balanced codes for edit errors
• On codes over \(\mathbb {F}_{q}+v\mathbb {F}_{q}+v^{2}\mathbb {F}_{q}\)

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