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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. California Institute of Technology , Pasadena, CA. (Unpublished)

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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 two families of codes for correcting errors due to tandem-duplications of a fixed length; the first family can correct any number of errors while the second corrects a bounded 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:Report or Paper (Technical Report)
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URLURL TypeDescription Paper
Jain, Siddharth0000-0002-9164-6119
Farnoud (Hassanzadeh), Farzad0000-0002-8684-4487
Schwartz, Moshe0000-0002-1449-0026
Bruck, Jehoshua0000-0001-8474-0812
Additional Information:This work was supported in part by the NSF Expeditions in Computing Program (The Molecular Programming Project).
Group:Parallel and Distributed Systems Group
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Record Number:CaltechAUTHORS:20160125-143414675
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:63940
Deposited On:26 Jan 2016 19:03
Last Modified:10 Nov 2021 23:23

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