Multi-objective evolutionary probe design based on thermo dynamic criteria for HPV detection

Abstract

DNA microarrays are widely used techniques in molecular biology and DNA computing area. It consists of the DNA sequences called probes, which are DNA complementaries to the genes of interest, on solid surfaces. And its reliability seriously depends on the quality of the probe sequences. Therefore, one must carefully choose the probe sets in target sequences. In this paper, the probe design for DNA microarrays is formulated as the multi-objective optimization problem. We propose a multi-objective evolutionary approach, which is known to be suitable for this kind of optimization problem. Since a multi-objective evolutionary algorithm can find multiple solutions at a time, we used thermodynamic criteria to choose the most suitable one. For the experiments, the probe set generated by the proposed method is compared to the sequences used in commercial microarrays, which detects a set of Human Papillomavirus (HPV). The comparison result supports that our approach can be useful to optimize probe sequences. © Springer-Verlag Berlin Heidelberg 2004.