Repetition coding as an effective error correction code for embedding information in DNA

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Title: Repetition coding as an effective error correction code for embedding information in DNA
Authors: Haughton, David
Balado, Félix
Permanent link: http://hdl.handle.net/10197/3405
Date: 24-Oct-2011
Abstract: The goal of DNA data embedding is to enable robust encoding of non-genetic information in DNA. This field straddles the areas of bioinformatics and digital communications, since DNA mutations can be seen as akin to a noisy channel from the point of view of information encoding. In this paper we present two algorithms which, building on a variant of a method proposed by Yachie et al., rely on repetition coding to effectively counteract the impact that mutations have on an embedded message. The algorithms are designed for resynchronising multiple, originally identical, information encoded DNA sequences, embedded within non-coding DNA (ncDNA) sections of a host genome. They use both BLAST and MUSCLE algorithms to accomplish this. Bit error rates at the decoder are established for mutations rates accumulated over a number of generations of the host organism. The empirical results obtained are compared to a theoretical bound for optimal decoding.
Funding Details: Science Foundation Ireland
Type of material: Conference Publication
Publisher: IEEE
Copyright (published version): 2011 IEEE
Keywords: DNA data wmbedding;Decoding performance;DNA watermarking;Sequence alignment
Subject LCSH: DNA
Data encryption (Computer science)
Digital watermarking
Sequence alignment (Bioinformatics)
DOI: 10.1109/BIBE.2011.45
Language: en
Status of Item: Peer reviewed
Is part of: 2011 IEEE 11th International Conference on Bioinformatics and Bioengineering (BIBE) [proceedings]
Conference Details: 11th IEEE International Conference on Bioinformatics and Bioengineering (BIBE), 24-26, October 2011, Taichung, Taiwan
Appears in Collections:Computer Science Research Collection

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