2016/06/07 by Ian Holmes · 5 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · Engineering · Mathematics · #Advanced biosensing and bioanalysis techniques #Algorithm #Computer science #DNA and Biological Computing #Interleaving #Mathematics #Modular Robots and Swarm Intelligence #String (physics) #cs.IT #math.IT
paper · pdf · doi:10.1101/057448
published in bioRxiv (Cold Spring Harbor Laboratory) (Cold Spring Harbor Laboratory) · Submitted to IEEE Transactions on Information Theory
openalex publication_date 2016/06/07 · arxiv created 2016/06/08 · arxiv updated 2016/11/18 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
1 Abstract We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by interleaving watermark and periodic marker signals; conversion from binary to ternary, quaternary or mixed-radix sequences via an efficient block code; encoding into a DNA sequence that avoids homopolymer, dinucleotide, or trinucleotide runs and other short local repeats; and detection/correction of errors (including local duplications, burst deletions, and substitutions) that are characteristic of DNA sequencing technologies. We present software implementing these codes, available at https://github.com/ihh/dnastore , with simulation results demonstrating that the generated DNA is free of short repeats and can be accurately decoded even in the presence of substitutions, short duplications and deletions.