Consolidating software tools for DNA microarray design and manufacturing

As the human genome project progresses and some microbial and eukaryotic genomes are recognized, a novel technology, DNA microarray (also called gene chip, biochip, gene microarray, and DNA chip) technology, has attracted increasing number of biologists, bioengineers and computer scientists recently. This technology promises to monitor the whole genome at once, so that researchers can study the whole genome on the global level and have a better picture of the expressions among millions of genes simultaneously. Today, it is widely used in many fields - disease diagnosis, gene classification, gene regulatory network, and drug discovery. We present a concatenated software solution for the entire DNA array flow exploring all steps of a consolidated software tool. The proposed software tool has been tested on Herpes B virus as well as simulated data. Our experiments show that the genomic data follow the pattern predicted by simulated data although the number of border conflicts (quality of the DNA array design) is several times smaller than for simulated data. We also report a trade-off between the number of border conflicts and the running time for several proposed algorithmic techniques employed in the physical design of DNA arrays.