论文信息 - Supersequences of Masks for Oligo-chips

Supersequences of Masks for Oligo-chips

On a very small surface, a chip, several thousands of oligonucleotides, can be synthesized using a mask technology. Given a set of oligos, the problems tackled here are: What is the minimum number of masks necessary to synthesize one copy of each oligo? How long will be the series of masks if each oligo is synthesized twice, such that the two copies are realized with two completely different series of masks? We establish that, for 20,000 oligos of 20 bases a single copy can be synthesized with around 67 masks and for two copies with less than the double.

Alain Guénoche | A. Guénoche

[1] Earl Hubbell,et al. Fidelity Probes for DNA Arrays , 1999, ISMB.

[2] S. P. Fodor,et al. Combinatorial chemistry--applications of light-directed chemical synthesis. , 1994, Trends in biotechnology.

[3] David Maier,et al. The Complexity of Some Problems on Subsequences and Supersequences , 1978, JACM.

[4] Esko Ukkonen,et al. The Shortest Common Supersequence Problem over Binary Alphabet is NP-Complete , 1981, Theor. Comput. Sci..

[5] Sven Rahmann. The shortest common supersequence problem in a microarray production setting , 2003, ECCB.

[6] Alberto Apostolico,et al. The longest common subsequence problem revisited , 1987, Algorithmica.

[7] Tao Jiang,et al. On the Approximation of Shortest Common Supersequences and Longest Common Subsequences , 1994, SIAM J. Comput..

[8] Tao Jiang,et al. On the Approximation of Shortest Common Supersequences and Longest Common Subsequences , 1995, SIAM J. Comput..

[9] Alain Guénoche. About the design of oligo-chips , 2005, Discret. Appl. Math..

[10] Robert W. Irving,et al. On the Worst-Case Behaviour of Some Approximation Algorithms for the Shortest Common Supersequence of k Strings , 1993, CPM.