DNA chip technology is a powerful tool for genetic research that utilizes nucleic acid hybridization techniques and recent advancements in computing technology to evaluate the mRNA expression profile of thousands of genes within a single experiment. It has proven to be an extremely valuable tool to efficiently utilize the enormous amount of information provided by the completion of numerous genome projects.

DNA chips are fabricated by high-speed robotics, generally on glass or nylon substrates, for which probes (oligonucleotides or cDNA fragments) with known identity are used to determine complementary binding, thus allowing massively parallel gene expression and gene discovery studies.

The core of DNA chip design is selection of a set probes, oligonucleotides or cDNA fragments, optimized from target sequences based on the criteria of

• Specificity of the hybridization with the target sequence
• Uniform melting temperature of the probes, and
• Secondary structure stability

We propose five strategies for efficient selection of probe sequences satisfying these criteria:

• Removal of exactly repetitive sequences: to efficiently find sequences appearing in more than one ORF, and remove them from candidates for probe sequences.
• Minimization of frequency of occurrence: to estimate the frequency of occurrence of a probe sequence based on the frequency of occurrence of all k-tuples consisting of a probe sequence. Only rarely occurring sequences are selected for probe candidates.
• Unifying melting temperature: to calculate the melting temperature of matching probe. The filter classifies probe sequences into fewest groups with a uniform melting temperature. All DNA probes on a chip surface are subjected to the same hybridization and wash conditions. So the uniform melting temperature minimizes false-positive and/or false-negative signals, making accurate target identification possible.
• Filtering secondary structure stability: to calculate the free energy of optimal secondary structure of probe. Stable intra-strand secondary structure of probe hinders rapid hybridization to a target sequence, resulting in extensive decrease of the signal intensity. This filter removes those unfavorable probe sequences.
• Minimization of Hamming distance: to calculate the minimum Hamming distance between a probe sequence and a target sequence. It examines the specificity of probe.

Research and development of the DNA chip technology has been mainly conducted by leading companies such as Affymetrix (http://www.affymetrix.com). Novel techniques for probe selection catering to various systems and biomedical applications are highly demanded. We propose to set up a dedicated webserver and develop a software system to implement our strategies for DNA chip design.