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HELIOS: High-speed sequence alignment in optics

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...

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Autores principales: Maleki, Ehsan, Akbari Rokn Abadi, Saeedeh, Koohi, Somayyeh
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9678324/
https://www.ncbi.nlm.nih.gov/pubmed/36409684
http://dx.doi.org/10.1371/journal.pcbi.1010665
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author Maleki, Ehsan
Akbari Rokn Abadi, Saeedeh
Koohi, Somayyeh
author_facet Maleki, Ehsan
Akbari Rokn Abadi, Saeedeh
Koohi, Somayyeh
author_sort Maleki, Ehsan
collection PubMed
description 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.
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spelling pubmed-96783242022-11-22 HELIOS: High-speed sequence alignment in optics Maleki, Ehsan Akbari Rokn Abadi, Saeedeh Koohi, Somayyeh PLoS Comput Biol Research Article 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. Public Library of Science 2022-11-21 /pmc/articles/PMC9678324/ /pubmed/36409684 http://dx.doi.org/10.1371/journal.pcbi.1010665 Text en © 2022 Maleki et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Maleki, Ehsan
Akbari Rokn Abadi, Saeedeh
Koohi, Somayyeh
HELIOS: High-speed sequence alignment in optics
title HELIOS: High-speed sequence alignment in optics
title_full HELIOS: High-speed sequence alignment in optics
title_fullStr HELIOS: High-speed sequence alignment in optics
title_full_unstemmed HELIOS: High-speed sequence alignment in optics
title_short HELIOS: High-speed sequence alignment in optics
title_sort helios: high-speed sequence alignment in optics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9678324/
https://www.ncbi.nlm.nih.gov/pubmed/36409684
http://dx.doi.org/10.1371/journal.pcbi.1010665
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