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

Abstract

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.

A Novel Method to Realize Optical Correlation Recognition Based on Neural Network

“…There are application reports in areas such as car-assisted driving, bioinformatics detection, and big data retrieval, etc. [1]- [5]. An optical matching filter is the key component to determine the recognition performance of an optical correlator.…”

Speeding up DNA sequence alignment by optical correlator

“…So far, various optical DNA alignment approaches 25,27,28,34 have been proposed to perform correlation on two signals or images for detecting exact match among DNA strings. Although there might be some edits in one sequence that mess up exact matching, there still exist a large similarity among DNA strings that must be founded.…”

“…So far, various approaches such as optical correlation 23 and Moiré matching techniques 24,25 have been proposed to perform DNA sequence alignment by the means of optical computing process. In correlation based methods, 23,[26][27][28] DNA sequence alignment is performed through an optical correlator to detect regions with high score of similarity (referred to as global alignment).…”

HELIOS: High-speed sequence alignment in optics

“…Accordingly, biophotonics develops optical techniques for biological developments [ 25 ]. In this manner, some methods have been accomplished recently, such as correlation-based methods [ 26 , 27 ], Fourier-Transform-based algorithms [ 28 , 29 ], HAWPOD [ 30 ], Moiré Technique [ 31 – 33 ], OptCAM [ 34 ], GAC [ 35 ], and SPOMF [ 36 ]. Some of them [ 26 – 29 ] address optical similarity measurement algorithms for sequence alignment by taking advantage of optical correlation and Fourier Transform.…”