Genome assembly using quantum and quantum-inspired annealing

Abstract Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements,...

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Autores principales:	A. S. Boev, A. S. Rakitko, S. R. Usmanov, A. N. Kobzeva, I. V. Popov, V. V. Ilinsky, E. O. Kiktenko, A. K. Fedorov
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/cf61a08b80104c41b8c32113e6ff983b
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spelling	oai:doaj.org-article:cf61a08b80104c41b8c32113e6ff983b2021-12-02T16:05:54ZGenome assembly using quantum and quantum-inspired annealing10.1038/s41598-021-88321-52045-2322https://doaj.org/article/cf61a08b80104c41b8c32113e6ff983b2021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88321-5https://doaj.org/toc/2045-2322Abstract Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the $$\phi $$ ϕ X 174 bacteriophage. Our results pave a way for a significant increase in the efficiency of solving bioinformatics problems with the use of quantum computing technologies and, in particular, quantum annealing might be an effective method. We expect that the new generation of quantum annealing devices would outperform existing techniques for de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.A. S. BoevA. S. RakitkoS. R. UsmanovA. N. KobzevaI. V. PopovV. V. IlinskyE. O. KiktenkoA. K. FedorovNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q A. S. Boev A. S. Rakitko S. R. Usmanov A. N. Kobzeva I. V. Popov V. V. Ilinsky E. O. Kiktenko A. K. Fedorov Genome assembly using quantum and quantum-inspired annealing
description	Abstract Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for de novo genome assembly, which is used for the analysis of genomic rearrangements, chromosome phasing, and reconstructing genomes without a reference, require solving tasks of high computational complexity. Here we demonstrate a method for solving genome assembly tasks with the use of quantum and quantum-inspired optimization techniques. Within this method, we present experimental results on genome assembly using quantum annealers both for simulated data and the $$\phi $$ ϕ X 174 bacteriophage. Our results pave a way for a significant increase in the efficiency of solving bioinformatics problems with the use of quantum computing technologies and, in particular, quantum annealing might be an effective method. We expect that the new generation of quantum annealing devices would outperform existing techniques for de novo genome assembly. To the best of our knowledge, this is the first experimental study of de novo genome assembly problems both for real and synthetic data on quantum annealing devices and quantum-inspired techniques.
format	article
author	A. S. Boev A. S. Rakitko S. R. Usmanov A. N. Kobzeva I. V. Popov V. V. Ilinsky E. O. Kiktenko A. K. Fedorov
author_facet	A. S. Boev A. S. Rakitko S. R. Usmanov A. N. Kobzeva I. V. Popov V. V. Ilinsky E. O. Kiktenko A. K. Fedorov
author_sort	A. S. Boev
title	Genome assembly using quantum and quantum-inspired annealing
title_short	Genome assembly using quantum and quantum-inspired annealing
title_full	Genome assembly using quantum and quantum-inspired annealing
title_fullStr	Genome assembly using quantum and quantum-inspired annealing
title_full_unstemmed	Genome assembly using quantum and quantum-inspired annealing
title_sort	genome assembly using quantum and quantum-inspired annealing
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/cf61a08b80104c41b8c32113e6ff983b
work_keys_str_mv	AT asboev genomeassemblyusingquantumandquantuminspiredannealing AT asrakitko genomeassemblyusingquantumandquantuminspiredannealing AT srusmanov genomeassemblyusingquantumandquantuminspiredannealing AT ankobzeva genomeassemblyusingquantumandquantuminspiredannealing AT ivpopov genomeassemblyusingquantumandquantuminspiredannealing AT vvilinsky genomeassemblyusingquantumandquantuminspiredannealing AT eokiktenko genomeassemblyusingquantumandquantuminspiredannealing AT akfedorov genomeassemblyusingquantumandquantuminspiredannealing
_version_	1718385177128861696

Genome assembly using quantum and quantum-inspired annealing

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