Loading...

High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network

Maleki, E ; Sharif University of Technology | 2017

535 Viewed
  1. Type of Document: Article
  2. DOI: 10.1364/JOSAA.34.001173
  3. Publisher: OSA - The Optical Society , 2017
  4. Abstract:
  5. This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool. © 2017 Optical Society of America
  6. Keywords:
  7. DNA ; Gene encoding ; Neural networks ; Basic local alignment search tools ; Genome sequences ; Global alignment ; Local sequence alignments ; Matching techniques ; Optical correlators ; Optical processing ; Parallel processing ; Alignment
  8. Source: Journal of the Optical Society of America A: Optics and Image Science, and Vision ; Volume 34, Issue 7 , 2017 , Pages 1173-1186 ; 10847529 (ISSN)
  9. URL: https://www.osapublishing.org/josaa/abstract.cfm?uri=josaa-34-7-1173