Speeding up DNA sequence alignment by optical correlator. (December 2018)

• Record Type: Journal Article
• Authors: Mozafari, Fereshte; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra
• Is Part Of: Optics & laser technology. Volume 108(2018)
• Page Start: 124
• Page End: 135
• Publication Date: 2018-12
• Subjects: Optical computing -- Metamaterial -- Fourier optics -- Bioinformatics -- DNA sequence alignment; Optics -- Periodicals; Lasers -- Periodicals; Electronic journals; 621.366
• DOI: 10.1016/j.optlastec.2018.06.027
• Languages: English
• ISSNs: 0030-3992

Abstract

Highlights: A DNA sequence alignment method taking parallel optical processing is proposed. Proposed optical structure is built upon metamaterial based optical correlators. Result shows better performance and accuracy over well-known BLAST algorithm. Proposed architecture reduces power consumption compared to an electrical computer. 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, referred to as windows, and then, extracts the peaks resulted from their cross-correlation with the reference sequence in parallel. Finally, to locate the edits, a simple algorithm utilizing number and location of the peaks is introduced to analyze the correlation outputs obtained from window-based DNA sequence comparison. As a novel implementation approach, we adopt multiple metamaterial-based optical correlators to optically implement the proposed parallel architecture, named as Window-based Optical Correlator (WOC). This wave-based computing architecture fully controls wave transmission and phase using dielectric and plasmonic materials. Design limitations and challenges of the proposed architecture are also discussed in details. The simulation results, comparing WOC with the well-known BLAST algorithm, demonstrate superior speed-up up to 60%, as well as, high accuracy even at the presence of large number of edits. Also, WOC method considerably reduces power consumption as a result of implementing metamaterial-based optical computing structure.