Journal
IEEE TRANSACTIONS ON INFORMATION THEORY
Volume 64, Issue 9, Pages 6283-6296Publisher
IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC
DOI: 10.1109/TIT.2018.2792488
Keywords
Biological information theory; constrained coding; channel coding; data storage systems; DNA-based data storage systems; bioinformatics
Funding
- NSF [CCF 16-18366]
- Singapore Ministry of Education [MOE2015-T2-2-086, MOE2016-T1-001-156]
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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.
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