Microarray probe design using ε-multi-objective evolutionary algorithms with thermodynamic criteria

Authors:
Soo-Yong Shin;In-Hee Lee;Byoung-Tak Zhang
Affiliations:
Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, Korea;Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, Korea;Biointelligence Laboratory, School of Computer Science and Engineering, Seoul National University, Seoul, Korea
Venue:
EuroGP'06 Proceedings of the 2006 international conference on Applications of Evolutionary Computing
Year:
2006

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Abstract

As DNA microarrays have been widely used for gene expression profiling and other fields, the importance of reliable probe design for microarray has been highlighted. First, the probe design for DNA microarray was formulated as a constrained multi-objective optimization task by investigating the characteristics of probe design. Then the probe set for human paillomavrius (HPV) was found using ε-multi-objective evolutionary algorithm with thermodynamic fitness calculation. The evolutionary optimization of probe set showed better results than the commercial microarray probe set made by Biomedlab Co. Korea.