Stochastic local search algorithms for DNA word design

Abstract

We present results on the performance of a stochastic local search algorithm for the design of DNA codes, namely sets of equal-length words over the nucleotides alphabet {A, C, G, T} that satisfy certain combinatorial constraints. Using empirical analysis of the algorithm, we gain insight on good design principles. We report several cases in which our algorithm finds word sets that match or exceed the best previously known constructions. © Springer-Verlag Berlin Heidelberg 2003.