Rates of DNA Sequence Profiles for Practical Values of Read Lengths

DOI10.1109/TIT.2017.2747557MaRDI QIDQ4566552zbMATH OpenOpenAlexFDO

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)

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)

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.

Cited in

(4)

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

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