Efficient Probe Selection in Microarray Design

The DNA microarray technology, originally developed to measure the level of gene expression, had become one of the most widely used tools in genomic study. Microarrays have been proved to benefit areas including gene discovery, disease diagnosis, and multi-virus discovery. The crux of microarray design lies in how to select a unique probe that distinguishes a given genomic sequence from other sequences. However, in cases that the existence of a unique probe is unlikely, e.g., in the context of a large family of closely homologous genes, the use of a limited number of non-unique probes is still desirable. Due to its significance, probe selection attracts a lot of attention. Various probe selection algorithms have been developed in recent years. Good probe selection algorithms should produce as small number of candidate probes as possible. Efficiency is also crucial because the data involved is usually huge. Most existing algorithms usually select probes by filtering, which is usually not selective enough and quite a large number of probes are returned. We propose a new direction to tackle the problem and give an efficient algorithm to select (randomly) a small set of probes and demonstrate that such a small set of probes is sufficient to distinguish each sequence from all the other sequences. Based on the algorithm, we have developed a probe selection software RandPS, which runs efficiently and effectively in practice. A number of experiments have been carried out and the results will be discussed