The Distribution and Deposition Algorithm for Multiple Oligo Nucleotide Arrays

Kang Ning (ningkang@comp.nus.edu.sg)
Hon Wai Leong (leonghw@comp.nus.edu.sg)

Department of Computer Science, National University of Singapore, 3 Science Drive 2 117543, Singapore


Abstract

As the scale of the microarray experiments increases, a single oligo nucleotide array is no longer large enough. Therefore, the use of multiple oligo arrays for one experiment becomes more important. The design and synthesis of multiple arrays to minimize the overall synthesis cost is an interesting and important problem. We formulate the multiple array synthesis problem (MASP) that deals with the distribution of the probes (or oligos) to different arrays, and then deposition of the probes onto each array. We propose a cost function to capture the synthesis cost and a performance ratio for analysis of the quality of multiple arrays produced by different algorithms. We propose a Distribution and Deposition Algorithm (DDA) for the solving the MASP. In this algorithm, the probes are first distributed onto multiple arrays according to their characteristics such as GC contents. Then the probes on each arrays are deposited using a good deposition algorithm. Two other algorithms were also proposed and used for comparison. Experiments show that our algorithm can effectively output short synthesis sequences for multiple arrays, and the algorithm is efficient.

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Japanese Society for Bioinformatics