• Journal of KIISE:Software and Applications
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• v.35 no.8
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• pp.501-511
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• 2008

Probe design is one of the essential tasks in successful DNA microarray experiments. The requirements for probes vary as the purpose or type of microarray experiments. In general, most previous works use the simple filtering approach with the fixed threshold value for each requirement. Here, we formulate the probe design as a multiobjective optimization problem with the two objectives and solve it using ${\epsilon}$-multiobjective evolutionary algorithm. The suggested approach was applied in designing probes for 19 types of Human Papillomavirus and 52 genes in Arabidopsis Calmodulin multigene family and successfully produced more target specific probes compared to well known probe design tools such as OligoArray and OligoWiz.