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Experimental construction of very large scale DNA databases with associative search capability

Publication ,  Conference
Reif, JH; LaBean, TH; Pirrung, M; Rana, VS; Guo, B; Kingsford, C; Wickham, GS
Published in: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
January 1, 2002

We describe on-going experiments for executing associative search queries within synthesized DNA databases. Queries are executed by hybridization of a target database strand with a complementary query strand probe. In our initial annealing experiments for processing associative search queries, we employed fluorescently labeled query strands and performed separation of fluorescent versus non-fluorescent beads using Fluorescence Activated Cell Sorting (FACS or flow cytometry). We also tested polymerase chain reaction (PCR) as an output method, and developed a PCR technique for search in the pair-wise constructed library that exploits the particular properties of words in that library. We have also implemented computer software that provides a simulation (viewable on the internet) of the experimental search procedures, as well as a simulation of input/output from conventional 2D images.

Duke Scholars

Published In

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

DOI

EISSN

1611-3349

ISSN

0302-9743

ISBN

3540437754

Publication Date

January 1, 2002

Volume

2340

Start / End Page

231 / 247

Related Subject Headings

  • Artificial Intelligence & Image Processing
  • 46 Information and computing sciences
 

Citation

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Reif, J. H., LaBean, T. H., Pirrung, M., Rana, V. S., Guo, B., Kingsford, C., & Wickham, G. S. (2002). Experimental construction of very large scale DNA databases with associative search capability. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 2340, pp. 231–247). https://doi.org/10.1007/3-540-48017-x_22
Reif, J. H., T. H. LaBean, M. Pirrung, V. S. Rana, B. Guo, C. Kingsford, and G. S. Wickham. “Experimental construction of very large scale DNA databases with associative search capability.” In Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2340:231–47, 2002. https://doi.org/10.1007/3-540-48017-x_22.
Reif JH, LaBean TH, Pirrung M, Rana VS, Guo B, Kingsford C, et al. Experimental construction of very large scale DNA databases with associative search capability. In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2002. p. 231–47.
Reif, J. H., et al. “Experimental construction of very large scale DNA databases with associative search capability.” Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2340, 2002, pp. 231–47. Scopus, doi:10.1007/3-540-48017-x_22.
Reif JH, LaBean TH, Pirrung M, Rana VS, Guo B, Kingsford C, Wickham GS. Experimental construction of very large scale DNA databases with associative search capability. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2002. p. 231–247.
Journal cover image

Published In

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

DOI

EISSN

1611-3349

ISSN

0302-9743

ISBN

3540437754

Publication Date

January 1, 2002

Volume

2340

Start / End Page

231 / 247

Related Subject Headings

  • Artificial Intelligence & Image Processing
  • 46 Information and computing sciences