DNA Microarray placement for improved performance and reliability

DNA Microarrays or DNA chips have become a standard method for identification of DNA sequence (genes or gene mutation), determination of abundance of genes and other genomic analysis. DNA Microarrays are composed of small DNA fragments (probes) which are manufactured using masks and photolithographic method similar to VLSI industry. However, photolithographic manufacturing technology introduces errors in the probes due to unintended illumination leading to reduced performance and reliability of the Microarray. In this paper, we present a placement method using a metric for performance of microarray. We propose a Hilbert-curve filling based probe placement which incorporates the performance metric. Experimental results show upto 57x increase in the hybridization potential (leading to higher performance and reliability) of the probes on using our method.