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Tytuł:
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Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture.
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Autorzy:
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Akbari Rokn Abadi S; Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
Hashemi Dijujin N; Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
Koohi S; Department of Computer Engineering, Sharif University of Technology, Tehran, Iran.
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Źródło:
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PloS one [PLoS One] 2021 Jan 15; Vol. 16 (1), pp. e0245095. Date of Electronic Publication: 2021 Jan 15 (Print Publication: 2021).
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Typ publikacji:
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Comparative Study; Journal Article
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Język:
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English
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Imprint Name(s):
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Original Publication: San Francisco, CA : Public Library of Science
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MeSH Terms:
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Algorithms*
Optics and Photonics*
Sequence Alignment*
Sequence Analysis, DNA*
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References:
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IEEE/ACM Trans Comput Biol Bioinform. 2017 May-Jun;14(3):634-645. (PMID: 26890922)
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Bioinformatics. 2010 May 1;26(9):1145-51. (PMID: 20208069)
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Entry Date(s):
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Date Created: 20210115 Date Completed: 20210510 Latest Revision: 20210510
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Update Code:
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20240105
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PubMed Central ID:
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PMC7810328
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DOI:
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10.1371/journal.pone.0245095
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PMID:
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33449928
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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.
Competing Interests: The authors have declared that no competing interests exist.
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