A Multi-objective Genetic Algorithm Based Approach to the Optimization of Oligonucleotide Microarray Production Process
Microarrays are becoming more and more utilized in the experimental platform in molecular biology. Although rapidly becoming affordable, these micro devices still have quite high production cost which limits their commercial appeal. Here we present a novel multiobjective evolutionary approach to the optimization of the production process of microarray devices mainly aimed at lowering the number of fabrication steps. In order to allow the reader to better understand what we describe we report herein a detailed description of a real-world study case carried out on the most recent microarray platforms of the market leader in this field. A comparative analysis of the most widely used approaches, main potentialities and drawbacks of the proposed approach are presented.
KeywordsPareto Front Deposition Sequence Microelectrode Array Microarray Production Photolithographic Mask
Unable to display preview. Download preview PDF.
- 2.Hannenhalli, S., Hubell, E., Lipshutz, R., Pevzner, P.A.: Combinatorial Algorithms for Design of DNA Arrays. Advances in Biochemical Engineering Biotechnology 77, 1–9 (2002)Google Scholar
- 3.Storer, J.A.: Data Compression: Methods and Theory. Computer Science Press (1988)Google Scholar
- 6.Cormen, T.H., Leiserson, C.E., Rivest, R.L., Stein, C.: Introduction to Algorithms, 2nd edn. MIT Press/McGraw-Hill (2001)Google Scholar
- 7.Sankoff, D., Kruskal, J.: Time Warps, String Edits and Macromolecules: the Theory and Practice of Sequence Comparisons. Addison Wesley, Reading (1983)Google Scholar
- 8.Barone, P., Bonizzoni, P., Vedova, G.D., Mauri, G.: An Approximation Algorithm for the Shortest Common Supersequence Problem: an Experimental Analysis. In: Symposium on Applied Computing, Proceedings of the 2001 ACM symposium on Applied computing, pp. 56–60 (2001)Google Scholar
- 11.Timkovsky, V.G.: On the Approximation of Shortest Common Non-subsequences and Supersequences. Technical report (1993)Google Scholar
- 12.Kasif, S., Weng, Z., Derti, A., Beigel, R., DeLisi, C.: A Computational Framework for Optimal Masking in the Synthesis of Oligonucleotide Microarrays. Nucleic Acids Research 30(20) (2002)Google Scholar
- 13.Irving, R.W., Fraser, C.: On the Worst-Case Behaviour of Some Approximation Algorithms for the Shortest Common Supersequence of k Strings. In: Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching, pp. 63–73 (1993)Google Scholar
- 14.Holland, J.H.: Adaptation in Natural and Artificial Systems. University of Michigan Press, Ann Arbor (1975)Google Scholar