Mining DNA Sequences Based on Spatially Coded Technique Using Spatial Light Modulator

Abstract: In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association information of the genome and the expressed phenotypes could more effectively be extracted. Such moire fringes reveal occurrence of matching, deletion and insertion between DNA sequences providing useful visualized information for prediction of gene function and classification of species. Furthermore, by applying a cylindrical lens, a new technique is proposed to map two-dimensional (2D) association information to a one-dimensional (1D) column of pixels, where each pixel in the column is representative of superposition of all bright and dark pixels in the corresponding row. By such a time-consuming preprocessing, local similarities between two intended patterns can readily be found by just using a 1D array of photodetectors and postprocessing could be performed on specified parts in the initial 2D pattern. We also evaluate our proposed circular encoding adapted for poor data alignment condition. Our simulation results together with experimental implementation verify the effectiveness of our dynamic proposed methods which significantly improve system parameters such as processing gain and signal to noise ratio (SNR).