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

TL;DR

This paper introduces a high-speed all-optical method for DNA sequence alignment using wavelength and polarization modulation, combining optical correlators with an extended DV-curve approach for faster genome analysis.

Contribution

It presents a novel all-optical implementation of the DV-curve based DNA alignment method, significantly improving speed over traditional electrical methods.

Findings

The optical method is much faster than electrical counterparts.

The accuracy of the optical approach is validated through numerical simulations.

The proposed system effectively performs global and local DNA sequence alignment.

Abstract

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 DV- curve 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.