eprintid: 796
rev_number: 16
eprint_status: archive
userid: 35
dir: disk0/00/00/07/96
datestamp: 2011-08-11 10:12:31
lastmod: 2013-03-05 15:42:26
status_changed: 2011-08-11 10:12:31
type: article
metadata_visibility: show
item_issues_count: 0
creators_name: Tsaftaris, Sotirios A.
creators_name: Katsaggelos, Aggelos K.
creators_id: sotirios.tsaftaris@imtlucca.it
creators_id: 
title: Retrieval efficiency of DNA-Based databases of digital signals
ispublished: pub
subjects: QA76
subjects: QH426
divisions: EIC
full_text_status: none
keywords: DNA based databases; DNA hybridization; digital signals; query; retrieval efficiency; similarity criterion; DNA; biocomputing; query formulation; query processing;algorithms; computers, molecular; databases, Genetic; in situ hybridization, fluorescence; information storage and retrieval; signal processing, computer-assisted;
abstract: Using DNA to store digital signals, or data in general, offers significant advantages when compared to other media. The DNA molecule, especially in its double-stranded form, is very stable, compact, and inexpensive. In the past, we have shown that DNA can be used to store and retrieve digital signals encoded and stored in DNA. We have also shown that DNA hybridization can be used as a similarity criterion for retrieving digital signals encoded and stored in a DNA database. Retrieval is achieved through hybridization of "query" and "data" DNA molecules. In this paper, we present a mathematical framework to simulate single-query and parallel-query scenarios, and to estimate hybridization efficiency. Our framework allows for exact numerical solutions as well as closed-form approximations under certain conditions. Similarly to the digital domain, we define a DNA SNR measure to assess the performance of the DNA-based retrieval scheme in terms of database size and source statistics. With approximations, we show that the SNR of any finite-sized DNA-based database is upper bounded by the SNR of an infinitely large DNA-based database that has the same source distribution. Computer simulations are presented to validate our results.
date: 2009-09
publication: IEEE Transactions on nanobioscience
volume: 8
number: 3
publisher: IEEE
pagerange: 259 -270
id_number: 10.1109/TNB.2009.2026371
refereed: TRUE
issn: 1536-1241
official_url: http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5161324&isnumber=5371771
citation:   Tsaftaris, Sotirios A. and Katsaggelos, Aggelos K.  Retrieval efficiency of DNA-Based databases of digital signals.  IEEE Transactions on nanobioscience, 8 (3).  259 -270.  ISSN 1536-1241      (2009)