Rates of DNA Sequence Profiles for Practical Values of Read Lengths

DOI10.1109/TIT.2017.2747557zbMATH Open1390.92097OpenAlexW2963545007MaRDI QIDQ4566552FDOQ4566552

Authors: Zuling Chang, Johan Chrisnata, Martianus Frederic Ezerman, Han Mao Kiah 

Publication date: 27 June 2018

Published in: IEEE Transactions on Information Theory (Search for Journal in Brave)

Abstract: A recent study by one of the authors has demonstrated the importance of profile vectors in DNA-based data storage. We provide exact values and lower bounds on the number of profile vectors for finite values of alphabet size $q$, read length $ell$, and word length $n$.Consequently, we demonstrate that for $qge2$ and $nle{q}^{ell/2-1}$, the number of profile vectors is at least $q^{kappan}$ with $kappa$ very close to one.In addition to enumeration results, we provide a set of efficient encoding and decoding algorithms for each of two particular families of profile vectors.

Full work available at URL: https://arxiv.org/abs/1607.02279

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Shift register sequences and sequences over finite alphabets in information and communication theory (94A55)

Cited In (4)

• Cut-down de Bruijn sequences
• On the \(k\)-error linear complexities of De Bruijn sequences
• Construction of de Bruijn sequences from product of two irreducible polynomials
• On the number of distinct \(k\)-decks: enumeration and bounds

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