Modular non-repeating codes for DNA storage

Ian Holmes

doi:10.1101/057448

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arXiv · 1606.01799

Modular non-repeating codes for DNA storage

Ian Holmes

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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 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.

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Ian Holmes. 2016-06-06. Modular non-repeating codes for DNA storage. https://doi.org/10.1101/057448

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