OptCAM: An ultra-fast all-optical architecture for DNA variant discovery.,Journal of Biophotonics

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OptCAM: An ultra-fast all-optical architecture for DNA variant discovery.
Journal of Biophotonics ( IF 2.0 ) Pub Date : 2019-08-29 , DOI: 10.1002/jbio.201900227
Ehsan Maleki ₁ , Somayyeh Koohi ₁ , Zahra Kavehvash ₂ , Alireza Mashaghi ₃

Affiliation

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 high‐speed processing and operational parallelism, inherently exist in optics. The proposed method, named as OptCAM, utilizes amplitude and wavelength of the optical signals, to accurately locate mutations through three main procedures. Furthermore, an all‐optical implementation of the OptCAM method is proposed consisting of three units, corresponding to the three OptCAM procedures. Performing considerably fast processes by passing optical signals through high‐throughput photonic devices, OptCAM avoids various limitations of electrical implementations. Accuracy and efficiency of the OptCAM method and its optical implementation are validated through numerical simulation by a gold standard simulation benchmark. The results indicate the proposed method is significantly faster than its electrical counterparts, in both single node and grid computation.

中文翻译：

OptCAM：用于DNA变异发现的超快速全光学架构。

如今，遗传数据的加速扩展由于其电子实现方式而挑战了当前DNA序列比对算法的速度。高效，准确的DNA变异发现方法的基本需求要求实时并行处理的新方法。幸运的是，作为一种新兴的数据计算技术，光子学提出将光相关作为一种快速的相似性测量算法。现有的局部比对算法的复杂性严重限制了它们的适用性。因此，在本文中，我们将光学相关性用于全局比对，我们提出了一种用于局部DNA序列比对的光学处理方法，以同时受益于光学中固有的高速处理和操作并行性。提议的方法称为OptCAM，利用光信号的振幅和波长，通过三个主要过程精确定位突变。此外，提出了由三个单元组成的，对应于三个OptCAM程序的OptCAM方法的全光学实现。OptCAM通过使光信号通过高通量光子器件来执行相当快的过程，从而避免了电气实施的各种限制。OptCAM方法及其光学实现的准确性和效率通过金标准仿真基准通过数值仿真得到了验证。结果表明，无论是在单节点计算还是在网格计算中，所提出的方法都比其电气方法快得多。提出了由三个单元组成的，对应于三个OptCAM程序的OptCAM方法的全光学实现。OptCAM通过使光信号通过高通量光子器件来执行相当快的过程，从而避免了电气实施的各种限制。OptCAM方法及其光学实现的准确性和效率通过金标准仿真基准通过数值仿真得到了验证。结果表明，无论是在单节点计算还是在网格计算中，所提出的方法都比其电气方法快得多。提出了由三个单元组成的，对应于三个OptCAM程序的OptCAM方法的全光学实现。OptCAM通过使光信号通过高通量光子器件来执行相当快的过程，从而避免了电气实施的各种限制。OptCAM方法及其光学实现的准确性和效率通过金标准仿真基准通过数值仿真得到了验证。结果表明，无论是在单节点计算还是在网格计算中，所提出的方法都比其电气方法快得多。OptCAM避免了电气实施的各种限制。OptCAM方法及其光学实现的准确性和效率通过金标准仿真基准通过数值仿真得到了验证。结果表明，无论是在单节点计算还是在网格计算中，所提出的方法都比其电气方法快得多。OptCAM避免了电气实施的各种限制。OptCAM方法及其光学实现的准确性和效率通过金标准仿真基准通过数值仿真得到了验证。结果表明，无论是在单节点计算还是在网格计算中，所提出的方法都比其电气方法快得多。

更新日期：2019-08-29

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