Fractal construction of constrained code words for DNA storage systems

The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. On...

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Autores principales: Löchel, Hannah F, Welzel, Marius, Hattab, Georges, Hauschild, Anne-Christin, Heider, Dominik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Methods Online
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934655/
https://www.ncbi.nlm.nih.gov/pubmed/34908135
http://dx.doi.org/10.1093/nar/gkab1209
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author Löchel, Hannah F
Welzel, Marius
Hattab, Georges
Hauschild, Anne-Christin
Heider, Dominik
author_facet Löchel, Hannah F
Welzel, Marius
Hattab, Georges
Hauschild, Anne-Christin
Heider, Dominik
author_sort Löchel, Hannah F
collection PubMed
description The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. One is to use DNA as a storage medium, and the other is to use DNA for computing. Both strategies come with certain constraints. In the current study, we present a novel approach derived from chaos game representation for DNA to generate DNA code words that fulfill user-defined constraints, namely GC content, homopolymers, and undesired motifs, and thus, can be used to build codes for reliable DNA storage systems.
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spelling pubmed-89346552022-03-21 Fractal construction of constrained code words for DNA storage systems Löchel, Hannah F Welzel, Marius Hattab, Georges Hauschild, Anne-Christin Heider, Dominik Nucleic Acids Res Methods Online The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are two main categories in which biological molecules, especially DNA, are investigated as alternatives to silicon-based computer technologies. One is to use DNA as a storage medium, and the other is to use DNA for computing. Both strategies come with certain constraints. In the current study, we present a novel approach derived from chaos game representation for DNA to generate DNA code words that fulfill user-defined constraints, namely GC content, homopolymers, and undesired motifs, and thus, can be used to build codes for reliable DNA storage systems. Oxford University Press 2021-12-15 /pmc/articles/PMC8934655/ /pubmed/34908135 http://dx.doi.org/10.1093/nar/gkab1209 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methods Online
Löchel, Hannah F
Welzel, Marius
Hattab, Georges
Hauschild, Anne-Christin
Heider, Dominik
Fractal construction of constrained code words for DNA storage systems
title Fractal construction of constrained code words for DNA storage systems
title_full Fractal construction of constrained code words for DNA storage systems
title_fullStr Fractal construction of constrained code words for DNA storage systems
title_full_unstemmed Fractal construction of constrained code words for DNA storage systems
title_short Fractal construction of constrained code words for DNA storage systems
title_sort fractal construction of constrained code words for dna storage systems
topic Methods Online
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934655/
https://www.ncbi.nlm.nih.gov/pubmed/34908135
http://dx.doi.org/10.1093/nar/gkab1209
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AT hattabgeorges fractalconstructionofconstrainedcodewordsfordnastoragesystems
AT hauschildannechristin fractalconstructionofconstrainedcodewordsfordnastoragesystems
AT heiderdominik fractalconstructionofconstrainedcodewordsfordnastoragesystems

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