13 research outputs found
On Critical Relative Distance of 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 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.Comment: 5 or 6 pages (compiler-dependable), 0 figures, submitted to 2010 IEEE
International Symposium on Information Theory (ISIT 2010), uses IEEEtran.cl
Reversible DNA codes from skew cyclic codes over a ring of order 256
We introduce skew cyclic codes over the finite ring , where and use them to construct reversible DNA codes. The 4-mers are matched with the elements of this ring. The reversibility problem for DNA 4-bases is solved and some examples are provided
On DNA codes from a family of chain rings
In this work, we focus on reversible cyclic codes which correspond to reversible DNA codes or reversible-complement DNA codes over a family of finite chain rings, in an effort to extend what was done by Yildiz and Siap in [20]. The ring family that we have considered are of size , and we match each ring element with a DNA -mer. We use the so-called -adic digit system to solve the reversibility problem and we characterize cyclic codes that correspond to reversible-complement DNA-codes. We then conclude our study with some examples