Vander Lugt correlation of DNA sequence data

William A. Christens-Barry; James F. Hawk; James C. Martin

doi:10.1117/12.23411

27 December 1990 Vander Lugt correlation of DNA sequence data

William A. Christens-Barry, James F. Hawk, James C. Martin

Proceedings Volume 1347, Optical Information Processing Systems and Architectures II; (1990) https://doi.org/10.1117/12.23411
Event: 34th Annual International Technical Symposium on Optical and Optoelectronic Applied Science and Engineering, 1990, San Diego, CA, United States

Abstract

DNA, the molecule containing the genetic code of an organism, is a linear chain of subunits. It is the sequence of subunits, of which there are four kinds, that constitutes the unique blueprint of an individual. This sequence is the focus of a large number of analyses performed by an army of geneticists, biologists, and computer scientists. Most of these analyses entail searches for specific subsequences within the larger set of sequence data. Thus, most analyses are essentially pattern recognition or correlation tasks. Yet, there are special features to such analysis that influence the strategy and methods of an optical pattern recognition approach. While the serial processing employed in digital electronic computers remains the main engine of sequence analyses, there is no fundamental reason that more efficient parallel methods cannot be used. We describe an approach using optical pattern recognition (OPR) techniques based on matched spatial filtering. This allows parallel comparison of large blocks of sequence data. In this study we have simulated a Vander Lugt1 architecture implementing our approach. Searches for specific target sequence strings within a block of DNA sequence from the Co/El plasmid2 are performed.

Citation Download Citation

William A. Christens-Barry, James F. Hawk, and James C. Martin "Vander Lugt correlation of DNA sequence data", Proc. SPIE 1347, Optical Information Processing Systems and Architectures II, (27 December 1990); https://doi.org/10.1117/12.23411

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