U.S. Department of Defense


Date of this Version



2010 IEEE International Symposium on Information Theory - Proceedings, 5513751, pp. 1325-1329.


© 2010 IEEE

This document is a U.S. government work and is not subject to copyright in the United States.

DOI: 10.1109/ISIT.2010.5513751


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 ”thermodynamic weights” associated to stacked pairs that occurred in DNA secondary structures.