Proceedings 21st International Conference on Computer Design (2003)
San Jose, California
Oct. 13, 2003 to Oct. 15, 2003
Andrew B. Kahng , University of California at San Diego
Ion I. Mandoiu , University of Connecticut
Sherief Reda , University of California at San Diego
Xu Xu , University of California at San Diego
Alex Z. Zelikovsky , Georgia State University
DNA probe arrays have recently emerged as one of the core genomic technologies. Exploiting analogies between manufacturing processes for DNA arrays and for VLSI chips, we demonstrate the potential for transfer of methodologies from the 40-year old field of electronic design automation to the newer DNA array design field. Our main contributions in this paper are the following. (1) We give a new design flow for DNA arrays which enhances current methodologies by adding flow-awareness to each optimization step and introducing feedback loops. (2) We propose solution methods for new formulations integrating multiple design steps, including probe selection, placement, and embedding. (3) We give results of a comprehensive experimental study showing that significant improvements in solution quality can be achieved by using the enhanced methodologies.
X. Xu, S. Reda, A. B. Kahng, A. Z. Zelikovsky and I. I. Mandoiu, "Design Flow Enhancements for DNA Arrays," Proceedings 21st International Conference on Computer Design(ICCD), San Jose, California, 2003, pp. 116.