eprintid: 791
rev_number: 22
eprint_status: archive
userid: 35
dir: disk0/00/00/07/91
datestamp: 2011-08-10 13:39:35
lastmod: 2013-03-05 15:48:37
status_changed: 2011-08-10 13:39:35
type: article
metadata_visibility: show
item_issues_count: 0
creators_name: Tsaftaris, Sotirios A.
creators_name: Hatzimanikati, Vassily
creators_name: Katsaggelos, Aggelos K.
creators_id: sotirios.tsaftaris@imtlucca.it
creators_id: 
creators_id: 
title: In silico estimation of annealing specificity of query searches in DNA databases
ispublished: pub
subjects: QA76
subjects: QH426
divisions: CSA
full_text_status: public
keywords: database; dna; dna_dsp
note: Special Issue "Application and Simulation of DNA Computing"
abstract: We consider DNA implementations of databases for digital signals with retrieval and mining capabilities. Digital signals are encoded in DNA sequences and retrieved through annealing between query DNA primers and data carrying DNA target sequences. The hybridization between query and target can be non-specific containing multiple mismatches thus implementing similarity-based searches. In this paper we examine theoretically and by simulation the efficiency of such a system by estimating the concentrations of query-target duplex formations at equilibrium. A coupled kinetic model is used to estimate the concentrations. We offer a derivation that results in an equation that is guaranteed to have a solution and can be easily and accurately solved computationally with bi-section root-finding methods. Finally, we also provide an approximate solution at dilute query concentrations that results in a closed form expression. This expression is used to improve the speed of the bi-section algorithm and also to find a closed form expression for the specificity ratios.
date: 2005-12
date_type: published
publication: Journal of the Japan society of simulation technology 
volume: 24
number: 4
publisher: Japan Society of Simulation Technology 
pagerange: 268-276
refereed: TRUE
issn: 0285-9947
related_url_url: http://ci.nii.ac.jp/naid/110004059524/en
related_url_type: pub
citation:   Tsaftaris, Sotirios A. and Hatzimanikati, Vassily and Katsaggelos, Aggelos K.  In silico estimation of annealing specificity of query searches in DNA databases.  Journal of the Japan society of simulation technology , 24 (4).  pp. 268-276.  ISSN 0285-9947      (2005)  
document_url: http://eprints.imtlucca.it/791/1/Tsaftaris_2005.pdf