Mining DNA sequences based on spatially coded technique using spatial light modulator

M. Fazelian, S. Abdollahramezani, S. Bahrani, A. Chizari, M.V. Jamali, P. Khorramshahi, A. Tashakori, S. Shahsavari, J.A. Salehi

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review


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 post-processing 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).
Original languageEnglish
Title of host publicationIWCIT 2016 - Iran Workshop on Communication and Information Theory
ISBN (Electronic)978-1-5090-1922-9
Publication statusPublished - 2016
Externally publishedYes
EventIran Workshop on Communication and Information Theory, IWCIT 2016 - Tehran, Iran, Islamic Republic of
Duration: 3 May 20164 May 2016


WorkshopIran Workshop on Communication and Information Theory, IWCIT 2016
Abbreviated titleIWCIT 2016
Country/TerritoryIran, Islamic Republic of


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