DNA hybridization as a similarity criterion for querying digital signals stored in DNA databases

S. A. Tsaftaris*, V. Hatzimanikatis, Aggelos K Katsaggelos

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

We demonstrate via simulation that hybridization of DNA molecules can be used as a similarity criterion for retrieving digital signals encoded and stored in a synthesized DNA database. After introducing some necessary DNA terminology, we briefly explain how digital signals are transformed to DNA sequences. Since retrieval is achieved through hybridization of query and data carrying DNA molecules, we present a mathematical model to estimate hybridization efficiency (also known as selectivity annealing). We show that selectivity annealing is inversely proportional to the mean squared error (MSE) of the encoded signal values. In addition, we show that the concentration of the molecules plays the same role as the decision threshold employed in digital signal matching algorithms. Finally, similar to the digital domain, we define a DNA signal-to-noise ratio (SNR) measure to assess the performance of the DNA-based retrieval scheme. Simulations are presented to validate our arguments.

Original languageEnglish (US)
Title of host publication2006 IEEE International Conference on Acoustics, Speech, and Signal Processing - Proceedings
StatePublished - Dec 1 2006
Event2006 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP 2006 - Toulouse, France
Duration: May 14 2006May 19 2006

Publication series

NameICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
Volume2
ISSN (Print)1520-6149

Other

Other2006 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP 2006
CountryFrance
CityToulouse
Period5/14/065/19/06

ASJC Scopus subject areas

  • Software
  • Signal Processing
  • Electrical and Electronic Engineering

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