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dna-sequency-alignment
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Speeding up DNA sequence alignment by optical correlator
, Article Optics and Laser Technology ; Volume 108 , 2018 , Pages 124-135 ; 00303992 (ISSN) ; Babashah, H ; Koohi, S ; Kavehvash, Z ; Sharif University of Technology
Elsevier Ltd
2018
Abstract
In electronic computers, extensive amount of computations required for searching biological sequences in big databases leads to vast amount of energy consumption for electrical processing and cooling. On the other hand, optical processing is much faster than electrical counterpart, due to its parallel processing capability, at a fraction of energy consumption level and cost. In this regard, this paper proposes a correlation-based optical algorithm using metamaterial, taking advantages of optical parallel processing, to efficiently locate the edits as a means of DNA sequence comparison. Specifically, the proposed algorithm partitions the read DNA sequence into multiple overlapping intervals,...
Design & Analysis of a DNA String Matching System Based on Optical Parallel Processing
, M.Sc. Thesis Sharif University of Technology ; Kavehvash, Zahra (Supervisor) ; Koohi, Somaie (Co-Advisor) ; Khavasi, Amin (Co-Advisor)
Abstract
In recent years, the biological evolution of molecular detection capabilities based on gene analysis has provided a reliable performance in the diagnosis of a disease before a symptom emerges. Human gene storage requires a large amount of computer memory (about 1.5 GB for each DNA) and the search for a specific pattern within it with electronic computers is time and power consuming. Optical computing uses light parallel processing capabilities to find the pattern in a digital field, which can be used to process large volumes of data in short time and low power consumption, while electronic computers process data in series with high power dissipation. According to the Optalysys report, the...
Design and Analysis of DNA Sequencing Methods
, Ph.D. Dissertation Sharif University of Technology ; Hossein Khalaj, Babak (Supervisor) ; Abolfazl, Motahhari (Co-Advisor)
Abstract
A DNA sequence is the information source of living kinds. Information of this sequence is at its constructing bases which has four different kinds. Sequencing DNA is necessary to resolve this information. At 1977, Sanger reported the first sequence of a DNA string. Recently, a human DNA string can be sequenced with 1000 in ~2 hours. Knowing DNA sequence helps to find function of each organism, predict and cure diseases (especially in cancer). Next Generation Sequencing (NGS) methods are based on shot-gun sequencing which fragmentize DNA strings and sequence each fragment. After sequencing, processing information of DNA is performed by the processing machine in two different types: alignment...
Design and Implementation of DNA Pattern Recognition Algorithm Utilizing Optical Coding Method
, M.Sc. Thesis Sharif University of Technology ; Koohi, Somayyeh (Supervisor) ; Kavehvash, Zahra (Supervisor)
Abstract
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...
OptCAM: An ultra-fast all-optical architecture for DNA variant discovery
, Article Journal of Biophotonics ; Volume 13, Issue 1 , August , 2020 ; Koohi, S ; Kavehvash, Z ; Mashaghi, A ; Sharif University of Technology
Wiley-VCH Verlag
2020
Abstract
Nowadays, the accelerated expansion of genetic data challenges speed of current DNA sequence alignment algorithms due to their electrical implementations. Essential needs of an efficient and accurate method for DNA variant discovery demand new approaches for parallel processing in real time. Fortunately, photonics, as an emerging technology in data computing, proposes optical correlation as a fast similarity measurement algorithm; while complexity of existing local alignment algorithms severely limits their applicability. Hence, in this paper, employing optical correlation for global alignment, we present an optical processing approach for local DNA sequence alignment to benefit both...