Empirical model-building and response surface
Empirical model-building and response surface
The Fidelity of Annealing-Ligation: A Theoretical Analysis
DNA '00 Revised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing
Complexity analysis of the SAT engine: DNA algorithms as probabilistic algorithms
Theoretical Computer Science - Natural computing
Universal Biochip Readout of Directed Hamiltonian Path Problems
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
A Software Tool for Generating Non-crosshybridizing Libraries of DNA Oligonucleotides
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Codeword design and information encoding in DNA ensembles
Natural Computing: an international journal
Physical modeling of biomolecular computers: Models, limitations, and experimental validation
Natural Computing: an international journal
Statistical thermodynamic analysis and designof DNA-based computers
Natural Computing: an international journal
International Journal of Knowledge-based and Intelligent Engineering Systems - Selected papers from the KES2004 conference
Designing nucleotide sequences for computation: a survey of constraints
DNA'05 Proceedings of the 11th international conference on DNA Computing
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In the universal DNA chip method, target RNAs are mapped onto a set of DNA tags. Parallel hybridization of these tags with an indexed, complementary antitag array then provides an estimate of the relative RNA concentrations in the original solution. Although both error estimation and error reduction are important to process application, a physical model of hybridization fidelity for the TAT system has yet to be proposed. In this work, an equilibrium chemistry model of TAT hybridation is used to estimate the error probability per hybridized tag (驴). The temperature dependence of 驴 is then discussed in detail, and compared with the predictions of the stringency picture. In combination with a modified statistical zipper model of duplex formation, implemented by the Mjolnir software package, 驴 is applied to investigate the error behavior of small to moderate sized TAT sets. In the first simulation, the fidelities of (1) 105 random encodings, (2) a recently reported Hamming encoding, and (3) an 驴-based, evolved encoding of a 32-strand, length- 16 TAT system are estimated, and discussed in detail. In the second simulation, the scaling behavior of the mean error rate of random TAT encodings is investigated. Results are used to discuss the ability of a random strategy to generate high fidelity TAT sets, as a function of set size and encoding length.