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

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  • Saeedeh Akbari Rokn Abadi
  • Negin Hashemi Dijujin
  • Somayyeh Koohi

Abstract

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.

Suggested Citation

  • Saeedeh Akbari Rokn Abadi & Negin Hashemi Dijujin & Somayyeh Koohi, 2021. "Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture," PLOS ONE, Public Library of Science, vol. 16(1), pages 1-27, January.
    • Handle: RePEc:plo:pone00:0245095
    DOI: 10.1371/journal.pone.0245095
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    References listed on IDEAS

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    1. Julie D Thompson & Benjamin Linard & Odile Lecompte & Olivier Poch, 2011. "A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives," PLOS ONE, Public Library of Science, vol. 6(3), pages 1-14, March.
    2. Millaray Curilem Saldías & Felipe Villarroel Sassarini & Carlos Muñoz Poblete & Asticio Vargas Vásquez & Iván Maureira Butler, 2012. "Image Correlation Method for DNA Sequence Alignment," PLOS ONE, Public Library of Science, vol. 7(6), pages 1-11, June.
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