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QuASeR: Quantum Accelerated de novo DNA sequence reconstruction
In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. This is the first time this important application in bioinformatics is modeled using quantum computation. Each one of the four step...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041170/ https://www.ncbi.nlm.nih.gov/pubmed/33844699 http://dx.doi.org/10.1371/journal.pone.0249850 |
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author | Sarkar, Aritra Al-Ars, Zaid Bertels, Koen |
author_facet | Sarkar, Aritra Al-Ars, Zaid Bertels, Koen |
author_sort | Sarkar, Aritra |
collection | PubMed |
description | In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. This is the first time this important application in bioinformatics is modeled using quantum computation. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with a proof-of-concept example to target both the genomics research community and quantum application developers in a self-contained manner. The implementation and results on executing the algorithm from a set of DNA reads to a reconstructed sequence, on a gate-based quantum simulator, the D-Wave quantum annealing simulator and hardware are detailed. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/QE-Lab/QuASeR. |
format | Online Article Text |
id | pubmed-8041170 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-80411702021-04-20 QuASeR: Quantum Accelerated de novo DNA sequence reconstruction Sarkar, Aritra Al-Ars, Zaid Bertels, Koen PLoS One Research Article In this article, we present QuASeR, a reference-free DNA sequence reconstruction implementation via de novo assembly on both gate-based and quantum annealing platforms. This is the first time this important application in bioinformatics is modeled using quantum computation. Each one of the four steps of the implementation (TSP, QUBO, Hamiltonians and QAOA) is explained with a proof-of-concept example to target both the genomics research community and quantum application developers in a self-contained manner. The implementation and results on executing the algorithm from a set of DNA reads to a reconstructed sequence, on a gate-based quantum simulator, the D-Wave quantum annealing simulator and hardware are detailed. We also highlight the limitations of current classical simulation and available quantum hardware systems. The implementation is open-source and can be found on https://github.com/QE-Lab/QuASeR. Public Library of Science 2021-04-12 /pmc/articles/PMC8041170/ /pubmed/33844699 http://dx.doi.org/10.1371/journal.pone.0249850 Text en © 2021 Sarkar 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 Sarkar, Aritra Al-Ars, Zaid Bertels, Koen QuASeR: Quantum Accelerated de novo DNA sequence reconstruction |
title | QuASeR: Quantum Accelerated de novo DNA sequence reconstruction |
title_full | QuASeR: Quantum Accelerated de novo DNA sequence reconstruction |
title_fullStr | QuASeR: Quantum Accelerated de novo DNA sequence reconstruction |
title_full_unstemmed | QuASeR: Quantum Accelerated de novo DNA sequence reconstruction |
title_short | QuASeR: Quantum Accelerated de novo DNA sequence reconstruction |
title_sort | quaser: quantum accelerated de novo dna sequence reconstruction |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8041170/ https://www.ncbi.nlm.nih.gov/pubmed/33844699 http://dx.doi.org/10.1371/journal.pone.0249850 |
work_keys_str_mv | AT sarkararitra quaserquantumaccelerateddenovodnasequencereconstruction AT alarszaid quaserquantumaccelerateddenovodnasequencereconstruction AT bertelskoen quaserquantumaccelerateddenovodnasequencereconstruction |