TY - JOUR
T1 - Duplication-Correcting Codes for Data Storage in the DNA of Living Organisms
AU - Jain, Siddharth
AU - Farnoud Hassanzadeh, Farzad
AU - Schwartz, Moshe
AU - Bruck, Jehoshua
N1 - Funding Information:
Manuscript received June 1, 2016; revised December 9, 2016; accepted March 13, 2017. Date of publication March 28, 2017; date of current version July 12, 2017. This work was supported by the NSF Expeditions in Computing Program (The Molecular Programming Project). This paper was presented at the 2016 IEEE International Symposium on Information Theory. (Corresponding Author: Siddharth Jain.) S. Jain and J. Bruck are with the Department of Electrical Engineering, California Institute of Technology, Pasadena, CA 91125 USA (e-mail: sidjain@caltech.edu; bruck@paradise.caltech.edu).
Funding Information:
Dr. Bruck is a recipient of the Feynman Prize for Excellence in Teaching, the Sloan Research Fellowship, the National Science Foundation Young Investigator Award, the IBM Outstanding Innovation Award and the IBM Outstanding Technical Achievement Award.
Publisher Copyright:
© 1963-2012 IEEE.
PY - 2017/8/1
Y1 - 2017/8/1
N2 - 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 are 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 $k=2,3$. Finally, we provide a full classification of the sets of lengths allowed in tandem duplication that result in a unique root for all sequences.
AB - 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 are 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 $k=2,3$. Finally, we provide a full classification of the sets of lengths allowed in tandem duplication that result in a unique root for all sequences.
KW - DNA
KW - Error-correcting codes
KW - string-duplication systems
KW - tandem-duplication errors
UR - http://www.scopus.com/inward/record.url?scp=85028987152&partnerID=8YFLogxK
U2 - 10.1109/TIT.2017.2688361
DO - 10.1109/TIT.2017.2688361
M3 - Article
AN - SCOPUS:85028987152
SN - 0018-9448
VL - 63
SP - 4996
EP - 5010
JO - IEEE Transactions on Information Theory
JF - IEEE Transactions on Information Theory
IS - 8
M1 - 7888471
ER -