Computationally inspired biotechnologies: Improved DNA synthesis and associative search using error-correcting codes and vector-quantization

Published

Conference Paper

© Springer-Verlag Berlin Heidelberg 2001. The main theme of this paper is to take inspiration from methods used in computer science and related disciplines, and to apply these to develop improved biotechnology. In particular, our proposed improvements are made by adapting various information theoretic coding techniques which originate in computational and information processing disciplines, but which we re-tailor to work in the biotechnology context. (a) We apply Error-Correcting Codes, developed to correct transmission errors in electronic media, to decrease (in certain contexts, optimally) error rates in optically-addressed DNA synthesis (e.g., of DNA chips). (b) We apply Vector-Quantization (VQ) Coding techniques (which were previously used to cluster, quantize, and compress data such as speech and images) to improve I/O rates (in certain contexts, optimally) for transformation of electronic data to and from DNA with bounded error. (c) We also apply VQ Coding techniques, some of which hierarchically cluster the data, to improve associative search in DNA databases by reducing the problem to that of exact afinity separation. These improvements in biotechnology appear to have some general applicability beyond biomolecular computing. As a motivating example, this paper improves biotechnology methods to do associative search in DNA databases. Baum [B95] previously proposed the use of biotechnology afinity methods (DNA annealing) to do massively parallel associative search in large databases encoded as DNA strands, but many remaining issues were not developed. Using in part our improved biotechnology techniques based on Error-Correction and VQ Coding, we develop detailed procedures for the following tasks: (i) The database may initially be in conventional (electronic, magnetic, or optical) media, rather than the form of DNA strands. For input and output (I/O) to and from conventional media, we apply DNA chip technology improved by Error-Correction and VQ Coding methods for error-correction and compression.

Full Text

Duke Authors

Cited Authors

  • Reif, JH; LaBean, TH

Published Date

  • January 1, 2001

Published In

Volume / Issue

  • 2054 /

Start / End Page

  • 145 - 172

Electronic International Standard Serial Number (EISSN)

  • 1611-3349

International Standard Serial Number (ISSN)

  • 0302-9743

International Standard Book Number 10 (ISBN-10)

  • 3540420762

International Standard Book Number 13 (ISBN-13)

  • 9783540420767

Digital Object Identifier (DOI)

  • 10.1007/3-540-44992-2_11

Citation Source

  • Scopus