New results on DNA codes for additive stem similarity

Author

Yachkov, A.D. ; Voronina, A. ; Alekseev, A. ; Sharonov, D.

Author_Institution

Dept. of Probability Theor., Moscow State Univ., Moscow, Russia

fYear

2010

Firstpage

34

Lastpage

39

Abstract

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.

Keywords

DNA; bioinformatics; molecular biophysics; molecular configurations; DNA code rate; DNA codes; DNA sequence hybridization potential; additive stem similarity; linear DNA code optimal construction; maximum distance separable codes; nearest neighbor similarity model; nearest neighbor thermodynamic weights; stem distance; thermodynamically motivated similarity measure; Additives; Construction industry; DNA; Markov processes; Region 8; Thermodynamics; Upper bound;

fLanguage

English

Publisher

ieee

Conference_Titel

Computational Technologies in Electrical and Electronics Engineering (SIBIRCON), 2010 IEEE Region 8 International Conference on

Conference_Location

Listvyanka

Print_ISBN

978-1-4244-7625-1

Type

conf

DOI

10.1109/SIBIRCON.2010.5555308

Filename

5555308