HELIOS: High-speed sequence alignment in optics.
Journal
PLoS computational biology
ISSN: 1553-7358
Titre abrégé: PLoS Comput Biol
Pays: United States
ID NLM: 101238922
Informations de publication
Date de publication:
11 2022
11 2022
Historique:
received:
01
01
2022
accepted:
18
10
2022
entrez:
21
11
2022
pubmed:
22
11
2022
medline:
24
11
2022
Statut:
epublish
Résumé
In response to the imperfections of current sequence alignment methods, originated from the inherent serialism within their corresponding electrical systems, a few optical approaches for biological data comparison have been proposed recently. However, due to their low performance, raised from their inefficient coding scheme, this paper presents a novel all-optical high-throughput method for aligning DNA, RNA, and protein sequences, named HELIOS. The HELIOS method employs highly sophisticated operations to locate character matches, single or multiple mutations, and single or multiple indels within various biological sequences. On the other hand, the HELIOS optical architecture exploits high-speed processing and operational parallelism in optics, by adopting wavelength and polarization of optical beams. For evaluation, the functionality and accuracy of the HELIOS method are approved through behavioral and optical simulation studies, while its complexity and performance are estimated through analytical computation. The accuracy evaluations indicate that the HELIOS method achieves a precise pairwise alignment of two sequences, highly similar to those of Smith-Waterman, Needleman-Wunsch, BLAST, MUSCLE, ClustalW, ClustalΩ, T-Coffee, Kalign, and MAFFT. According to our performance evaluations, the HELIOS optical architecture outperforms all alternative electrical and optical algorithms in terms of processing time and memory requirement, relying on its highly sophisticated method and optical architecture. Moreover, the employed compact coding scheme highly escalates the number of input characters, and hence, it offers reduced time and space complexities, compared to the electrical and optical alternatives. It makes the HELIOS method and optical architecture highly applicable for biomedical applications.
Identifiants
pubmed: 36409684
doi: 10.1371/journal.pcbi.1010665
pii: PCOMPBIOL-D-22-00001
pmc: PMC9678324
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e1010665Informations de copyright
Copyright: © 2022 Maleki et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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