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In silico estimation of annealing specificity of query searches in DNA databases

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)

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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.

Item Type: Article
Additional Information: Special Issue "Application and Simulation of DNA Computing"
Uncontrolled Keywords: database; dna; dna_dsp
Subjects: Q Science > QA Mathematics > QA76 Computer software
Q Science > QH Natural history > QH426 Genetics
Research Area: Computer Science and Applications
Depositing User: Users 35 not found.
Date Deposited: 10 Aug 2011 13:39
Last Modified: 05 Mar 2013 15:48
URI: http://eprints.imtlucca.it/id/eprint/791

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