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Noise and Uncertainty in String-Duplication Systems

Jain, Siddharth and Farnoud (Hassanzadeh), Farzad and Schwartz, Moshe and Bruck, Jehoshua (2017) Noise and Uncertainty in String-Duplication Systems. California Institute of Technology , Pasadena, CA. (Unpublished)

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Duplication mutations play a critical role in the generation of biological sequences. Simultaneously, they have a deleterious effect on data stored using in-vivo DNA data storage. While duplications have been studied both as a sequence-generation mechanism and in the context of error correction, for simplicity these studies have not taken into account the presence of other types of mutations. In this work, we consider the capacity of duplication mutations in the presence of point-mutation noise, and so quantify the generation power of these mutations. We show that if the number of point mutations is vanishingly small compared to the number of duplication mutations of a constant length, the generation capacity of these mutations is zero. However, if the number of point mutations increases to a constant fraction of the number of duplications, then the capacity is nonzero. Lower and upper bounds for this capacity are also presented. Another problem that we study is concerned with the mismatch between code design and channel in data storage in the DNA of living organisms with respect to duplication mutations. In this context, we consider the uncertainty of such a mismatched coding scheme measured as the maximum number of input codewords that can lead to the same output.

Item Type:Report or Paper (Technical Report)
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URLURL TypeDescription ItemPublished Version
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:20170119-133807104
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:73557
Deposited On:19 Jan 2017 21:44
Last Modified:18 Aug 2021 01:08

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