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© IRL Press at Oxford University Press

A knowledge-based experimental design system for nucleic acid engineering

K. Jiang 1,*, J. Z Heng 1,6, S. B. Higgins 1,2, D. M. Watterson 3,5, T. A. Craig 3,5, T. J. Lukas 3,5 and L. J. Van Eldik 3,4,5

1Departments of Biomedical Engineering,Vanderbilt University Nashville, TN 37232, USA
2Departments of Medicine,Vanderbilt University Nashville, TN 37232, USA
3Departments of Pharmacology,Vanderbilt University Nashville, TN 37232, USA
4Departments of Cell Biology,Vanderbilt University Nashville, TN 37232, USA
5Departments of Howard Hughes Medical Institute,Vanderbilt University Nashville, TN 37232, USA

*To whom reprint requests should be sent

Presented in this paper is a knowledge-based experimental design system that incorporates the domain expertise used in nucleic acid engineering, thus automating the processing of error-prone, laborious low-level work, and many decision-making steps, and guiding the biologist toward a workable plan. This allows the biologist to work at a higher abstraction level, concentrating on more fundamental, difficult and challenging problems directly related to protein structure-function relationships. Cassette-based site-directed mutagenesis and synthetic gene designs are used as examples to illustrate the utility of the knowledge-based system approach to experimental design.


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