Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture

Akbari Rokn Abadi, S ; Sharif University of Technology | 2021

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  1. Type of Document: Article
  2. DOI: 10.1371/journal.pone.0245095
  3. Publisher: NLM (Medline) , 2021
  4. Abstract:
  5. In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome, we can improve sensitivity and speed more than 86% and 81%, respectively, compared to BLAST by using coding set generated by GAC method fed to the proposed optical correlator system. Moreover, we present a comprehensive report on the impact of 1D and 2D cross-correlation approaches, as-well-as various coding parameters on the output noise, which motivate the system designers to customize the coding sets within the optical setup
  6. Keywords:
  7. Algorithm ; Comparative study ; DNA sequence ; Optics ; Sequence alignment ; Algorithms ; Optics and Photonics ; Sequence Alignment ; Sequence Analysis, DNA
  8. Source: PloS one ; Volume 16, Issue 1 , 2021 , Pages e0245095- ; 19326203 (ISSN)
  9. URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245095