Fractal construction of constrained code words for DNA storage systems

Abstract 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 technol...

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Published inNucleic acids research Vol. 50; no. 5; p. e30
Main Authors Löchel, Hannah F, Welzel, Marius, Hattab, Georges, Hauschild, Anne-Christin, Heider, Dominik
Format Journal Article
LanguageEnglish
Published England Oxford University Press 21.03.2022
Subjects
Computational Biology - methods
DNA
Fractals
Methods Online
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Abstract Abstract 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. Graphical Abstract Graphical Abstract Fractal construction of constrained code words for DNA storage systems.
AbstractList Abstract 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. Graphical Abstract Graphical Abstract 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. 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.
Abstract 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.
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. Graphical Abstract Fractal construction of constrained code words for DNA storage systems.
Author Hauschild, Anne-Christin
Heider, Dominik
Welzel, Marius
Löchel, Hannah F
Hattab, Georges
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Snippet Abstract The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science....
The use of complex biological molecules to solve computational problems is an emerging field at the interface between biology and computer science. There are...
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SubjectTerms Computational Biology - methods
DNA
Fractals
Methods Online
Title Fractal construction of constrained code words for DNA storage systems
URI https://www.ncbi.nlm.nih.gov/pubmed/34908135
https://search.proquest.com/docview/2610413541
https://pubmed.ncbi.nlm.nih.gov/PMC8934655
Volume 50
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