Design and Implementation of DNA Pattern Recognition Algorithm Utilizing Optical Coding Method

Maleki, Ehsan | 2017

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 49912 (19)
  4. University: Sharif University of Technology
  5. Department: Computer Engineering
  6. Advisor(s): Koohi, Somayyeh; Kavehvash, Zahra
  7. Abstract:
  8. In this research, two novel optical methods have been proposed for DNA local sequence alignment. The proposed methods benefit from algorithms and methods in computer field and ability of parallelism in optical wave to achieve a low-cost process and propose an easy understanding output in DNA local sequence alignment procedure. The first method is built upon moiré matching technique which is extended by proposed HAPPOC scheme using amplitude, phase, and polarization of optical wave. For analyzing the extended moiré output, a novel 3D Artificial Neural Network is designed and developed by optical structure. The second structure, as named HAWPOD method, is based on DV-Curve method. The HAWPOD method present an easy understanding output in four parts: HAWPOD coding, HAWPOD aligning, simplification, and improvement. The HAWPOD method is develop by an optical structure. The proposed methods are simulated in MATLAB, ZEMAX, and COMSOL framework. The output accuracy of proposed methods is also evaluated. Moreover, a traditional moiré matching technique is implemented physically to evaluate the accuracy of proposed method in implementation phase. The results express the proposed optical method improve the response time more than 99% in comparison with a well-known algorithm such as Basic Local Alignment Search Tool in electrical supercomputers
  9. Keywords:
  10. Optical Bioanformatic ; Local DNA Sequence Alignment ; Optical Computing ; Optical Coding ; Optical Moire Matching Technigue ; Three Dimentional Optical Artificial Neural Network ; HOWPOD Method

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