Rates of DNA Sequence Profiles for Practical Values of Read Lengths

2016/07/08 by Zuling Chang, Johan Chrisnata, Chang, Zuling +5
Biochemistry, Genetics and Molecular Biology · Computer Science · Mathematics · #Advanced biosensing and bioanalysis techniques #Algorithms and Data Compression #Combinatorics (math.CO) #DNA and Biological Computing #FOS: Computer and information sciences #FOS: Mathematics #Information Theory (cs.IT) #cs.IT #math.CO #math.IT

paper · pdf · doi:10.48550/arxiv.1607.02279

arxiv created 2016/07/08 · openalex publication_date 2016/07/08 · arxiv updated 2016/07/11 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

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 ℓ, and word length n.Consequently, we demonstrate that for q≥ 2 and n≤ q^ℓ/2-1, the number of profile vectors is at least q^κn with κ 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.

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