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Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms

Jain, Siddharth and Farnoud (Hassanzadeh), Farzad and Schwartz, Moshe and Bruck, Jehoshua (2016) Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms. In: 2016 IEEE International Symposium on Information Theory (ISIT). IEEE , Piscataway, NJ. ISBN 978-1-5090-1806-2.

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The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors arising from various mutations, such as point mutations, indels, and tandem duplication, which need to be corrected to maintain data integrity. In this paper, we provide error-correcting codes for errors caused by tandem duplications, which create a copy of a block of the sequence and insert it in a tandem manner, i.e., next to the original. In particular, we present a family of codes for correcting errors due to tandem-duplications of a fixed length and any number of errors. We also study codes for correcting tandem duplications of length up to a given constant k, where we are primarily focused on the cases of k = 2, 3.

Item Type:Book Section
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URLURL TypeDescription ItemTechnical Report
Jain, Siddharth0000-0002-9164-6119
Farnoud (Hassanzadeh), Farzad0000-0002-8684-4487
Schwartz, Moshe0000-0002-1449-0026
Bruck, Jehoshua0000-0001-8474-0812
Additional Information:© 2016 IEEE. This work was supported in part by the NSF Expeditions in Computing Program (The Molecular Programming Project).
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Record Number:CaltechAUTHORS:20160823-165024070
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:69869
Deposited By: Kristin Buxton
Deposited On:23 Aug 2016 23:58
Last Modified:11 Nov 2021 04:21

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