In this study, a new genetic algorithm was developed to discover the best motifs in a set of DNA sequences. The main steps were: finding the potential positions in each sequence by using few voters (1–5 sequences), constructing the chromosomes from the potential positions, evaluating the fitness for each gene (position) and for each chromosome, calculating the new random distribution, and using the new distribution to generate the next generation. To verify the effectiveness of the proposed algorithm, several real and artificial datasets were used; the results are compared to the standard genetic algorithm, and Gibbs, MEME, and consensus algorithms. Although all the algorithms have low correlation with the correct motifs, the new algorithm exhibits higher accuracy, without sacrificing implementation time.
A multi-objective genetic algorithm with side effect machines for motif discovery