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Experiment of Coding for DNA Data Storage.md

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Experiment of Coding for DNA Data Storage

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Part 1

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The following four fundamental problems of the DNA channel had to be tackled

  1. Error propagation: A single swap error, should alter bits after demodulation as little as possible. This allows efficient protection of the oligo addresses with a bit-correcting BCH code for a given redundancy.

  2. Run-length limitation: Because a sequence of more than 3 identical nucleotides may cause diffi- culties during sequencing of the oligos, the maximum run-length of identical nucleotides shall be limited to 3.

  3. Insertion and deletion errors: Since these two error types are quite common for today’s synthesiz- ers and sequencers, means for detecting and correcting insertion and deletion errors are manda- tory.

  4. Self-reverse complementariness: Self-reverse complimentary sections within a DNA molecule, potentially causing amplification issues of the corresponding oligo, had to be avoided.

Mapping of bit-tupels to nucleotides

Mapping of bit-tupels to nucleotides

In order to limit the maximum run-length of identical nucleotides to 3 for any possible combinations of DNA symbols, we defined the following constraints resulting in valid DNA symbols:

  • The first three nucleotides shall not be the same
  • The two last nucleotides shall not be the same

Insertion and deletion detection based on the use of alternating clusters for the DNA symbols

Insertion and deletion detection based on the use of alternating clusters for the DNA symbols

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