Mutually Uncorrelated Primers for DNA-Based Data Storage
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Ryan Gabrys, Olgica, Milenkovic
TL;DR
This paper introduces weakly mutually uncorrelated (WMU) sequences for DNA data storage, ensuring minimal overlap and error correction, with bounds and constructions for optimal code design.
Contribution
It defines WMU sequences with specific constraints and provides bounds and new constructions for balanced, error-correcting WMU codes in DNA data storage.
Findings
Derived bounds on WMU code sizes
Constructed balanced, error-correcting WMU codes
Proposed methods to avoid primer-dimer byproducts
Abstract
We introduce the notion of weakly mutually uncorrelated (WMU) sequences, motivated by applications in DNA-based data storage systems and for synchronization of 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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