DNA Codes Based on Stem Similarities Between DNA Sequences

Authors

Arkadii D'yachkov, Moscow State UniversityFollow
Anthony Macula, Air Force Res. Lab., IFTC, Rome Research SiteFollow
Vyacheslav Rykov, University of Nebraska at OmahaFollow
Vladimir Ufimtsev, University of Nebraska at Omaha

Document Type

Article

Date of this Version

2008

Citation

LNCS 4848, pp. 146–151, 2008

Comments

© Springer-Verlag Berlin Heidelberg 2008

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

Abstract

DNA codes consisting of DNA sequences are necessary for DNA computing. The minimum distance parameter of such codes is a measure of how dissimilar the codewords are, and thus is indirectly a measure of the likelihood of undetectedable or uncorrectable errors occurring during hybridization. To compute distance, an abstract metric, for example, longest common subsequence, must be used to model the actual bonding energies of DNA strands. In this paper we continue the development [1,2,3] of similarity functions for q-ary n-sequences The theoretical lower bound on the maximal possible size of codes, built on the space endowed with this metric, is obtained. that can be used (for q = 4) to model a thermodynamic similarity on DNA sequences. We introduce the concept of a stem similarity function and discuss DNA codes [2] based on the stem similarity. We suggest an optimal construction [2] and obtain random coding bounds on the maximum size and rate for such codes.