Constrained Coding with Error Control for DNA-Based Data Storage

In this paper, we first propose coding techniques for DNA-based data storage which account the maximum homopolymer runlength and the GC-content. In particular, for arbitrary l, epsilon > 0, we propose simple and efficient (epsilon, l)-constrained encoders that transform binary sequences into DNA base sequences (codewords), that satisfy the following properties: Runlength constraint: the maximum homopolymer run in each codeword is at most l, GC-content constraint: the GC-content of each codeword is within [0.5 - epsilon, 0.5 + l]. For practical values of l and epsilon, our codes achieve higher rates than the existing results in the literature. We further design efficient (epsilon, l)-constrained codes with error-correction capability. Specifically, the designed codes satisfy the runlength constraint, the GC-content constraint, and can correct a single edit (i.e. a single deletion, insertion, or substitution) and its variants. To the best of our knowledge, no such codes are constructed prior to this work.