Detection of DNA sequence symmetries using parallel micro-optical devices

William A. Christens-Barry; David H. Terry; Bradley G. Boone

doi:10.1117/12.49708

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1 November 1991 Detection of DNA sequence symmetries using parallel micro-optical devices

William A. Christens-Barry, David H. Terry, Bradley G. Boone

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Proceedings Volume 1564, Optical Information Processing Systems and Architectures III; (1991) https://doi.org/10.1117/12.49708
Event: San Diego, '91, 1991, San Diego, CA, United States

Abstract

In order to search for symbolically encoded sequences of DNA base information, we have constructed an incoherent optical feature extraction system. This approach uses video display, spatial light modulation, and detection components in conjunction with microlenslet replicating optics, to expedite the recognition of symbol sequences based on their symmetry properties. Multichannel operation is achieved through the replication of input scenery, making possible a higher throughput rate than for single channel systems. A notable feature of our arrangement has been the exchanged positions of input scenery and the filter set. The conventional treatment has been to display the input scene on a monitor for projection onto a set of feature extraction vectors realized as amplitude modulated LCTV devices or lithographically prepared masks. We have chosen instead to provide the filter set as input to the system and to correspondingly place the sequence data in the filter plane of the system, relying on the commutativity of projection to allow this role reversal. A class of DNA sequences known as palindromes are known to have special regulatory functions in biological systems; this class is distinguished by the antisymmetric arrangement of bases in palindromic sequences. We have designed our optical feature extractor to classify short (6 bases in length) sequences of DNA as palindrome or nonpalindrome. We note that this classification is made on the basis of the sequence symmetry, independent of base composition. We discuss the design of this architecture and the considerations that led us to the sequence representation. Initial results of this work are presented. Finally, the integration of this optical architecture into a complete system is discussed.

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William A. Christens-Barry, David H. Terry, and Bradley G. Boone "Detection of DNA sequence symmetries using parallel micro-optical devices", Proc. SPIE 1564, Optical Information Processing Systems and Architectures III, (1 November 1991); https://doi.org/10.1117/12.49708

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