Molecular and DNA Storage Coding
Stub. Coding theory for molecular (DNA-based) data storage: the basics of why and how DNA is used as a storage medium, the DNA storage channel's distinctive error profile (synthesis/sequencing errors, strand shuffling), and avoiding problematic sequences via constrained coding (and a glance at related DNA-encoded image processing).
Corresponds to Lecture topic 12. DNA is an extraordinarily dense and durable storage medium, which has driven interest in coding theory specifically adapted to it. Covers the basics of DNA-based data storage (how data is encoded into, synthesized as, and later sequenced back out of DNA strands), the DNA storage channel’s error profile — dominated by insertions, deletions, and substitutions during synthesis/sequencing, and by strands being read back in a scrambled (unordered, duplicated, or dropped) multiset rather than a single ordered sequence, which is exactly the regime deletion-correcting-codes-and-trace-reconstruction‘s machinery applies to — and constrained coding to avoid biologically problematic substrings (e.g. long homopolymer runs, which are synthesis/sequencing error-prone). Touches on DNA-based image processing as an application-level illustration of encoding richer, structured data into this medium.
Outline (TODO — flesh out each)
- DNA-based data storage — basics
- The DNA storage channel and its error profile
- Avoiding problematic (forbidden) substrings in DNA sequences
- Image processing in DNA