Summary
The conflicts between several design objectives for PCR primers are computationally resolved by specifying a set of ideal parameters and searching for primer pairs whose parameters approximate this ideal point as close as possible. It thus becomes feasible to identify an “optimum” and to efficiently compute it. User-specified target regions, primer conditions, and procedural conditions are obeyed.
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References
Keeney, R.L. and Raiffa, H. (1976) Decisions with Multiple Objectives. Wiley, New York.
Yu, P.L. (1989) Multiple criteria decision making: five basic concepts, in Handbooks in OR and Management Science I (Nemhauser, G. et al. eds.), North-Holland, Amsterdam, 663–699.
Kim, K.H. and Kim, Y. (2004) Variational transition state theory calculations for the rate constants of the hydrogen scrambling and the dissociation of BH_5 using the multiconfiguration molecular mechanics algorithm. The Journal of Chemical Physics 120, 623–630.
Mullis, K.B. and Faloona, F.A. (1987) Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology 155, 335–350.
Sahdra, B. and Thagard, P. (2003) Procedural knowledge in molecular biology. Philosophical Psychology 16, 477–498.
Kämpke, T., Kieninger, M. and Mecklenburg, M. (2001) Efficient primer design algorithms. Bioinformatics 17, 214–225.
Breslauer, K.J., Frank, R., Blocker, H. and Marky, L.A. (1986) Predicting DNA duplex stability from the base sequence. Proceedings of the National Academy of Sciences of the United States of America 83, 3746–3750.
Rychlik, W., Spencer, W.J. and Rhoads, R.E. (1990) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Research 18, 6409–6412.
Owczarzy, R., Vallone, P.M., Gallo, F.J., Paner, T.M., Lane, M.J. and Benight, A.S. (1997) Predicting sequence-dependent melting stability of short duplex DNA oligomers. Biopolymers 44, 217–239.
Thein, S.L. and Wallace, R.B. (1986) The use of synthetic oligonucleotides as specific hybridization probes in the diagnosis of genetic disorder, in Human Genetic Diseases: A Practical Approach (Davis, K.E. ed.), IRL Pres, Herndon.
Hillier, L. and Green, P. (1991) OSP: A computer program for predictions of DNA duplex stability. PCR Methods and Applications 1, 124–128.
Fleury, G., Hero, A., Yoshida, S., Carter, T., Barlow, C. and Swaroop, A. (2002) Pareto analysis for gene filtering in microarray experiments. Proceedings of the 11th European Signal Processing Conference, Toulouse.
Prezioso, V.R. (2005) General notes on primer design in PCR. Eppendorf North America, Westbury, http://www.eppendorfna.com.
Yuryev, A., Huang, J., Pohl, M., Patch, R., Watson, F., Bell, P., Donaldson, M., Phillips, M.S. and Boyce-Jacino, M.T. (2002) Predicting the success of primer extension genotyping assays using statistical modeling. Nucleic Acids Research 30, e131.
Tusnady, G.E., Simon, I., Varadi, A. and Aranyi, T. (2005) BiSearch: primer-design and search tool for PCR on bisulfite-treated genomes. Nucleic Acids Research 33, e9.
Huang, Y.-C., Chang, C.F., Chan, C.H., Yeh, T.J., Chang, Y.C., Chen, C.C. and Kao, C.Y. (2005) Integrated minimum-set primers and unique probe design algorithms for differential detection on symptom-related pathogens. Bioinformatics 21, 4330–4337.
Agrafiotis, D.K. (2001) Multiobjective optimization of combinatorial libraries. IBM Journal of Research and Development 45, 545–566.
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Kämpke, T. (2007). The Reference Point Method in Primer Design. In: Yuryev, A. (eds) PCR Primer Design. Methods in Molecular Biology™, vol 402. Humana Press. https://doi.org/10.1007/978-1-59745-528-2_4
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DOI: https://doi.org/10.1007/978-1-59745-528-2_4
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