Abstract: The aim of the paper is to show how the suitable codification of genes can help to the correct resolution of a problem using DNA computations. Genes are the income data of the problem to solve so the first task to carry out is the definition of the genes in order to perform a complete computation in the best way possible. In this paper we propose a model of encoding data into DNA strands so that this data can be used in the simulation of a genetic algorithm based on molecular operations. The first problem when trying to apply an algorithm in DNA computing must be how to codify the data that the algorithm will use. With preciseness, the gene formation exposed in this paper allows us to join the codification and evaluation steps in one single stage. Furthermore, these genes turn out to be stable in a DNA soup because we use bond-free languages in their definition. Previous work on DNA coding defined bond-free languages which several properties assuring the stability of any DNA word of such a language. We prove that a bond-free language is necessary but not sufficient to codify a gene giving the correct codification. That is due to the fact that selection must be done based on a concrete gene characterization. This characterization can be developed in many different ways codifying what we call the fitness field of the gene. It is shown how to use several DNA computing procedures based on genes from single and double stranded molecules to more complex DNA structures like plasmids.

Keywords: DNA Computing, Bond-Free? Languages, Genetic Algorithms, Gene Computing.

ACM Classification Keywords: I.6. Simulation and Modeling, B.7.1 Advanced Technologies, J.3 Biology and Genetics

Link:

GENE CODIFICATION FOR NOVEL DNA COMPUTING PROCEDURES

Angel Goni Moreno, Paula Cordero, Juan Castellanos

http://foibg.com/ijita/vol16/IJITA16-3-p01.pdf