Encoding Information for DNA computing. Shinnosuke Seki. Purpose. What’s an advantage of encoding? To make a “ good ” or tractable code set for DNA computing. Development of polynomial-time algorithms which decide whether a given code set is “good” or “bad”. Claude Elwood Shannon.
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Encoding Information for DNA computing
Information flow R
5’ - A T C G G T C A A C T G C C C T A A T G 3’
3’ T A G C C A G T T G A C G G G A T T A C - 5’
can form a (complete) dsDNA.
1 -> 2
2 -> 3
3 -> 4
Refer to [AlSa97], [TKY04] (,  in this table)
Template contains the same # of 0’s and 1’s (50% GC-content)
Map is an error correcting code.
Map is constant weight codes (50% GC-content)
Results in the bigger set of sequences
Hairpin frame (multiple loop)
A C G T
G C C
x v y θ(v) z
Input: A nondeterministic automaton M,
Output: Y/N depending on whether L(M) is hp(θ, k)-free.
Input: A deterministic automaton M1, and NFA M2.
Output: Y/N depending on whether there is a word
s.t. is hp(θ, k)-free.