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Proceedings Paper

Vander Lugt correlation of DNA sequence data
Author(s): William A. Christens-Barry; James F. Hawk; James C. Martin
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Paper 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.

Paper Details

Date Published: 27 December 1990
PDF: 10 pages
Proc. SPIE 1347, Optical Information Processing Systems and Architectures II, (27 December 1990); doi: 10.1117/12.23411
Show Author Affiliations
William A. Christens-Barry, Johns Hopkins Univ. (United States)
James F. Hawk, Univ. of Alabama/Birmingham (United States)
James C. Martin, Univ. of Alabama/Birmingham (United States)

Published in SPIE Proceedings Vol. 1347:
Optical Information Processing Systems and Architectures II
Bahram Javidi, Editor(s)

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