Rates of DNA Sequence Profiles for Practical Values of Read Lengths

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 1, and word length n. Consequently, we demonstrate that for q ≥ 2 and n ≤ q <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2-1</sup> , the number of profile vectors is at least q <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">κn</sup> with κ very close to 1. In addition to enumeration results, we provide a set of efficient encoding and decoding algorithms for certain families of profile vectors.