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

Fazelian, M ; Sharif University of Technology | 2016

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  1. Type of Document: Article
  2. DOI: 10.1109/IWCIT.2016.7491627
  3. Publisher: Institute of Electrical and Electronics Engineers Inc , 2016
  4. Abstract:
  5. 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)
  6. Keywords:
  7. Spatial light modulator ; String data alignment ; Alignment ; Classification (of information) ; Computation theory ; DNA ; DNA sequences ; Encoding (symbols) ; Gene encoding ; Genes ; Information theory ; Moire fringes ; Nucleic acids ; Optical data processing ; Pixels ; Signal to noise ratio ; Cylindrical lens ; Data alignments ; DNA Sequencing ; Local similarity ; Moire pattern ; Spatial encoding ; Spatial light modulators ; Two Dimensional (2 D) ; Light modulators
  8. Source: IWCIT 2016 - Iran Workshop on Communication and Information Theory, 3 May 2016 through 4 May 2016 ; 2016 ; 9781509019229 (ISBN)
  9. URL: http://ieeexplore.ieee.org/document/7491627