Dynamic Sliding Window Encoding for Data Storage on DNA Under Biological and Indexing Constraints

Abstract

In this paper, we propose a first dynamic sliding window encoding (DSWE) for storing encrypted data in a DNA form taking into account biological constraints and prohibited nucleotide motifs used for data indexing. Its originality is twofold. First, it takes advantage of variable length DNA codewords to avoid homopolymers longer than N bases when encoding binary data. Second, it relies on a sliding window to prevent the creation of prohibited motifs of nucleotides, adding non-coding bases when necessary. Contrarily to existing schemes, scaling DSWE to high values of N and of numbers of prohibited motifs is extremely simple. It is furthermore independent of the cryptosystem. We provide the theoretical information rate of our proposal for a given number of prohibited motifs and a maximum homopolymer length. Experiments show that in general, it offers much higher performances than existing schemes.