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Paper IDM.9.1
Paper Title Thermodynamically Stable DNA Code Design using a Similarity Significance Model
Authors Yixin Wang, Nanyang Technological University, Singapore; Noor-A-Rahim Md, University College Cork, Ireland; Erry Gunawan, Yong Liang Guan, Nanyang Technological University, Singapore; Chueh Loo Poh, National University of Singapore, Singapore
Session M.9: Topics in Coding for Storage and Memories
Presentation Lecture
Track Coding for Storage and Memories
Manuscript  Click here to download the manuscript
Virtual Presentation  Click here to watch in the Virtual Symposium
Abstract DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization affinities (or stabilities) of perfect double helix constructed by individual single-stranded DNA (ssDNA) and its RC pair, we propose a novel similarity significance (SS) model to measure the similarity between DNA sequences. Particularly, instead of directly measuring the similarity of two sequences by any metric/approach, the proposed SS works in a way to evaluate how more likely will the undesirable hybridizations occur over the desirable hybridizations in the presence of the two measured sequences and their RC pairs. With this SS model, we construct thermodynamically stable DNA codes subject to several combinatorial constraints using a sorting-based algorithm. The proposed scheme results in DNA codes with larger code sizes and wider free energy gaps (hence better cross-hybridization performance) compared to the existing methods.

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2021 IEEE International Symposium on Information Theory

11-16 July 2021 | Melbourne, Victoria, Australia

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