On Critical Relative Distance of DNA Codes for Additive Stem Similarity

Authors

A. D'yachkov, Moscow State UniversityFollow
A. Voronina, Moscow State UniversityFollow
Anthony Macula, Air Force Res. Lab., IFTC, Rome Research SiteFollow
T. Renz, Air Force Res. Lab., IFTC, Rome Research SiteFollow
Vyacheslav Rykov, University of Nebraska at OmahaFollow

Date of this Version

2010

Citation

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

Comments

© 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

Abstract

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.