Skip to main content
Article thumbnail
Location of Repository

Design flow enhancements for DNA arrays

By Andrew B. Kahng, Ion I. Măndoiu, Sherief Reda, Xu Xu and Alex Z. Zelikovsky

Abstract

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.

Year: 2003
OAI identifier: oai:CiteSeerX.psu:10.1.1.189.2035
Provided by: CiteSeerX
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://citeseerx.ist.psu.edu/v... (external link)
  • http://vlsicad.ucsd.edu/Public... (external link)
  • Suggested articles


    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.