Improved Genetic Algorithm for Designing DNA Sequences

Designing DNA sequences is one of the most practical and important research topics in DNA computing. An improved genetic algorithm for designing of the equal-length single-stranded DNA sequences is proposed, especially for the short DNA sequences needed in the DNA computing experiment. This algorithm can satisfy certain combinatorial and thermodynamic constraints such as GC content constraint, Hamming distance constraint and similarity constraint. It can generate the good short DNA sequences quickly by giving up the bad sequences in every generation. Finally, through analyzing the experiment data, two formulas are given to estimate the number of the DNA sequences satisfied GC content constraint and Hamming distance constraint.