High Speed All-optical extended DV-Curve-based DNA sequence alignment utilizing wavelength and polarization modulation

This paper presents a novel optical processing approach for exploring genome sequences built upon optical correlator for global alignment and extended DV-curve method for local alignment. To overcome the problem of traditional DV-curve method for presenting an accurate and simplified output, we propose HAWPOD, built upon DVcurve method, to analyze genome sequences in five steps: DNA coding, alignment, noise cancellation, simplification, and modification. Moreover, all-optical implementation of the HAWPOD method is developed, while its accuracy is validated through numerical simulations in LUMERICAL FDTD. The results express the proposed method is much faster than its electrical counterparts, such as Basic Local Alignment Search Tools.