Quantum DNA Sequencing using Gaussian Amplitude Amplification

Abstract: In this study, we explore how quantum pathfinding algorithm called Gaussian Amplitude Amplification (GAA) can be used to solve the DNA sequencing problem. To do this, sequencing by hybridization was assumed wherein short fragments of the nucleic acids called oligonucleotides of length l were gathered and were then assembled. The process of reassembling the sequence was then abstracted into a graph problem of finding the Hamiltonian path with the least cost. The constructed directed graph was then converted into sequential bipartite graphs in order to use GAA. The results of our simulation revealed that for the case where l = 2 and spectrum size of |S| = 4, the probability of finding the optimal solution (with the least cost) is approximately 70.92% - a significant improvement compared to 4.17% when the path is chosen randomly. While this study only focused on the ideal scenario where there are no errors in the spectrum, the outcomes presented here demonstrate the plausibility of using GAA as a genome sequencing method.