Mutually Uncorrelated Primers for DNA-Based Data Storage

We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization between communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of th...

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Published inIEEE transactions on information theory Vol. 64; no. 9; pp. 6283 - 6296
Main Authors Tabatabaei Yazdi, S. M. H., Kiah, Han Mao, Gabrys, Ryan, Milenkovic, Olgica
Format Journal Article
LanguageEnglish
Published New York IEEE 01.09.2018
The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subjects
bioinformatics
Biological information theory
Block codes
channel coding
constrained coding
Data storage
Data storage systems
Deoxyribonucleic acid
Dimers
DNA
DNA-based data storage systems
Electronic devices
Error correction
Gene sequencing
Hamming distance
Memory
Storage systems
Synchronism
Synchronization
Online AccessGet full text
ISSN0018-9448
1557-9654
DOI10.1109/TIT.2018.2792488

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Abstract We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization between communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized, and cyclic codes.
AbstractList We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization between communication devices. WMU sequences are characterized by the property that no sufficiently long suffix of one sequence is the prefix of the same or another sequence. WMU sequences used for primer design in DNA-based data storage systems are also required to be at large mutual Hamming distance from each other, have balanced compositions of symbols, and avoid primer-dimer byproducts. We derive bounds on the size of WMU and various constrained WMU codes and present a number of constructions for balanced, error-correcting, primer-dimer free WMU codes using Dyck paths, prefix-synchronized, and cyclic codes.
Author Tabatabaei Yazdi, S. M. H.
Gabrys, Ryan
Kiah, Han Mao
Milenkovic, Olgica
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Snippet We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and synchronization...
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SubjectTerms bioinformatics
Biological information theory
Block codes
channel coding
constrained coding
Data storage
Data storage systems
Deoxyribonucleic acid
Dimers
DNA
DNA-based data storage systems
Electronic devices
Error correction
Gene sequencing
Hamming distance
Memory
Storage systems
Synchronism
Synchronization
Title Mutually Uncorrelated Primers for DNA-Based Data Storage
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