An Efficient Two-Phase Algorithm to Find Gene-Specific Probes for Large Genomes

The accuracy of a DNA microarray is fairly dependent on the quality of probes it uses. Good probes should be specific to the respective target to avoid any cross-hybridization. Checking the specificity of a probe candidate is the most time-consuming task. We propose an efficient two-phase approach for finding gene- specific probes. At the first phase, for each gene our approach screens out other genes which have substrings that cause probe candidates of the gene to be bad. At the second phase, it exactly filters out bad probe candidates of each gene by comparing to the screened genes. In the case of S. cerevisiae having 6343 genes, our preprocessing algorithm took about 28minutes to screen out all other genes for every gene guaranteeing more than 95% of accuracy. And filtering algorithm took less than one minute to find all gene- specific probes of all genes.