An efficient algorithm for finding gene-specific probes for DNA microarrays

Abstract

The accuracy of a DNA microarray is fairly dependent on the quality of the probes it uses; a good probe should be specific for exactly one gene. Most sequence based algorithms use the edit distance to the target sequences as the measure of the specificity of the probe. We propose a novel algorithm for finding gene-specific probes which avoids large amounts of redundant computations of the edit distance, while maintaining the same accuracy as that provided by an exhaustive search. Our approach utilizes the fact that when the starting position of a probe candidate is moved only a few base pairs, the change in the edit distance to the off-target sequence is limited. The proposed algorithm does not use any index structures and is insensitive to the length of the probes. Our approach enables short (20-30 bases) or long (50 or more bases) probes to be computed for genomes of size 10M within a day. © Springer-Vorlag Berlin Heidelberg 2007.