EvoOligo: oligonucleotide probe design with multiobjective evolutionary algorithms

Authors:
Soo-Yong Shin;In-Hee Lee;Young-Min Cho;Kyung-Ae Yang;Byoung-Tak Zhang
Affiliations:
Medical Information Center, Seoul National University Hospital, Seoul, Korea;Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, Korea;University of California San Diego, La Jolla, CA;Center for Bioinformation Technology, Seoul National University, Seoul, Korea;Biointelligence Laboratory and the Center for Bioinformation Technology, School of Computer Science and Engineering, Seoul National University, Seoul, Korea
Venue:
IEEE Transactions on Systems, Man, and Cybernetics, Part B: Cybernetics
Year:
2009

Citing 6
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Abstract

Probe design is one of the most important tasks in successful deoxyribonucleic acid microarray experiments. We propose a multiobjective evolutionary optimization method for oligonucleotide probe design based on the multiobjective nature of the probe design problem. The proposed multiobjective evolutionary approach has several distinguished features, compared with previous methods. First, the evolutionary approach can find better probe sets than existing simple filtering methods with fixed threshold values. Second, the multiobjective approach can easily incorporate the user's custom criteria or change the existing criteria. Third, our approach tries to optimize the combination of probes for the given set of genes, in contrast to other tools that independently search each gene for qualifying probes. Lastly, the multiobjective optimization method provides various sets of probe combinations, among which the user can choose, depending on the target application. The proposed method is implemented as a platform called EvoOligo and is available for service on the web. We test the performance of EvoOligo by designing probe sets for 19 types of Human Papillomavirus and 52 genes in the Arabidopsis Calmodulin multigene family. The design results from EvoOligo are proven to be superior to those from well-known existing probe design tools, such as OligoArray and OligoWiz.