TY  - JOUR
A1  - Tsaftaris, Sotirios A.
A1  - Hatzimanikati, Vassily
A1  - Katsaggelos, Aggelos K.
PB  - Japan Society of Simulation Technology 
SP  - 268
Y1  - 2005/12//
JF  - Journal of the Japan society of simulation technology 
IS  - 4
VL  - 24
SN  - 0285-9947
N2  - 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.
AV  - public
TI  - In silico estimation of annealing specificity of query searches in DNA databases
KW  - database; dna; dna_dsp
UR  - http://eprints.imtlucca.it/791/
N1  - Special Issue "Application and Simulation of DNA Computing"
ID  - eprints791
EP  - 276
ER  -