We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the “hybridization potential” of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a thermodynamically motivated similarity measure called an additive stem similarity. These results yield a method to analyze and compare known samples of the nearest neighbor “thermo-dynamic weights” associated to stacked pairs that occurred in DNA secondary structures.

We consider DNA codes based on the concept of a weighted 2-stem similarity measure which reflects the ldquohybridization potentialrdquo of two DNA sequences. A random coding bound on the rate of DNA codes with respect to a thermodynamic motivated similarity measure is proved. Ensembles of DNA strands whose sequence composition is restricted in a manner similar to the restrictions in binary Fibonacci sequences are introduced to obtain the bound.

We introduce the distance concept between two q-ary n-sequences, 2/spl les/q

Kautz-Singleton (1964) suggested a class of binary superimposed codes which are based on the q-ary Reed-Solomon codes (RS codes). Applying a concatenation of the binary constant-weight error-correcting codes and the shortened RS codes, we obtain new constructions of superimposed codes. Tables of their parameters are given. From the tables it follows that the rate of obtained codes exceeds the corresponding random coding bound.