Combinatorial Algorithms for Design of DNA Arrays
Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination (border length minimization problem) and reducing the complexity of masks (mask decomposition problem). We describe algorithms that reduce the number of rectangles in mask decomposition by 20–30% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs.
KeywordsDNA arrays Photolitography Mask design Combinatorial algorithms Rectangle cover problem
Unable to display preview. Download preview PDF.
- 4.Cormen TH, Leiserson CE, Rivest RL (1990) Introduction to Algorithms. MIT PressGoogle Scholar
- 7.Garey MS, Johnson DS (1979) Computers and Intractibility: A Guide to the Theory of NP-Completeness. W H. Freeman, San Francisco, CAGoogle Scholar
- 10.Ohtsuki, T (1982) Minimum dissection of rectilinear regions. Proc. 1982 IEEE Symp. on Circuits and Systems 1210Google Scholar
- 11.Pevzner PA (2000) Computational Molecular Biology: An Algorithmic Approach. The MIT Press insteadGoogle Scholar
- 13.Wang DG, Fan J, Siao C, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris M, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson T, Lipshutz R, Chee M, Lander E (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077CrossRefGoogle Scholar