Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures

The characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts. We present a graph convolutional network-based deep learning framework for predicting kmer characteristic ionic currents from corresponding chemical structures. We show such a framework...

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Detalles Bibliográficos
Autores principales: Ding, Hongxu, Anastopoulos, Ioannis, Bailey, Andrew D., Stuart, Joshua, Paten, Benedict
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8586022/
https://www.ncbi.nlm.nih.gov/pubmed/34764310
http://dx.doi.org/10.1038/s41467-021-26929-x
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author Ding, Hongxu
Anastopoulos, Ioannis
Bailey, Andrew D.
Stuart, Joshua
Paten, Benedict
author_facet Ding, Hongxu
Anastopoulos, Ioannis
Bailey, Andrew D.
Stuart, Joshua
Paten, Benedict
author_sort Ding, Hongxu
collection PubMed
description The characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts. We present a graph convolutional network-based deep learning framework for predicting kmer characteristic ionic currents from corresponding chemical structures. We show such a framework can generalize the chemical information of the 5-methyl group from thymine to cytosine by correctly predicting 5-methylcytosine-containing DNA 6mers, thus shedding light on the de novo detection of nucleotide modifications.
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spelling pubmed-85860222021-11-15 Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures Ding, Hongxu Anastopoulos, Ioannis Bailey, Andrew D. Stuart, Joshua Paten, Benedict Nat Commun Article The characteristic ionic currents of nucleotide kmers are commonly used in analyzing nanopore sequencing readouts. We present a graph convolutional network-based deep learning framework for predicting kmer characteristic ionic currents from corresponding chemical structures. We show such a framework can generalize the chemical information of the 5-methyl group from thymine to cytosine by correctly predicting 5-methylcytosine-containing DNA 6mers, thus shedding light on the de novo detection of nucleotide modifications. Nature Publishing Group UK 2021-11-11 /pmc/articles/PMC8586022/ /pubmed/34764310 http://dx.doi.org/10.1038/s41467-021-26929-x Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Ding, Hongxu
Anastopoulos, Ioannis
Bailey, Andrew D.
Stuart, Joshua
Paten, Benedict
Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
title Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
title_full Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
title_fullStr Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
title_full_unstemmed Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
title_short Towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
title_sort towards inferring nanopore sequencing ionic currents from nucleotide chemical structures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8586022/
https://www.ncbi.nlm.nih.gov/pubmed/34764310
http://dx.doi.org/10.1038/s41467-021-26929-x
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