New results on DNA codes for additive stem similarity

We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the ”hybridization potential” of two DNA sequences. Our first aim is to discuss some optimal constructions of linear DNA codes called maximum distance separable (MDS) codes for stem distance. These constructions are compared with conventional MDS codes for Hamming distance. Our second 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. The given bounds yield a method to analyze and compare known samples of the nearest neighbor ”thermodynamic weights” associated to stacked pairs that occurred in DNA secondary structures.