Efficient Explicit and Pseudo-Random Constructions of Constrained Codes for DNA Storage

GC-content and homopolymers are two constraints widely considered in DNA storage. Extensive experiments show that DNA strings with too high/low GC-content and/or long homopolymers are more likely to suffer from errors. We say a length-n DNA string satisfies the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(\epsilon ,\ell)$ </tex-math></inline-formula>-constraints if no homopolymer exceeds <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\ell $ </tex-math></inline-formula> and its GC-content falls between <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(0.5-\epsilon)n$ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(0.5+\epsilon)n$ </tex-math></inline-formula>, where <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\epsilon $ </tex-math></inline-formula> is a positive real number and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\ell $ </tex-math></inline-formula> is a positive integer; say it satisfies the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(\delta ,\ell)$ </tex-math></inline-formula>-prefix-constraints if no homopolymer exceeds <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\ell $ </tex-math></inline-formula> and the GC-content of its length-i prefix falls between <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$i/2-\delta $ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$i/2+\delta $ </tex-math></inline-formula> for any <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$i \in \{1, 2, \ldots , n\}$ </tex-math></inline-formula>, where <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\delta $ </tex-math></inline-formula> is a positive integer. In this paper, we realize the first enumerative coding for the capacity-achieving <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(\epsilon ,\ell)$ </tex-math></inline-formula>-constrained codes and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(\delta ,\ell)$ </tex-math></inline-formula>-prefix-constrained codes with polynomial encoding/decoding complexity. Meanwhile, we propose an efficient pseudo-random construction of capacity-approaching <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(\epsilon ,\ell)$ </tex-math></inline-formula>-constrained codes and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$(\epsilon ,\ell)$ </tex-math></inline-formula>-constrained error correction codes. We further generalize the idea and establish a systematic framework of pseudo-random construction for a wide range of codes.