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DNA Hash Pooling and its Applications

DNA Hash Pooling and its Applications

Dennis Shasha, Martyn Amos
Copyright: © 2011 |Pages: 13
ISBN13: 9781609601867|ISBN10: 1609601866|EISBN13: 9781609601881
DOI: 10.4018/978-1-60960-186-7.ch002
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MLA

Shasha, Dennis, and Martyn Amos. "DNA Hash Pooling and its Applications." Theoretical and Technological Advancements in Nanotechnology and Molecular Computation: Interdisciplinary Gains, edited by Bruce MacLennan, IGI Global, 2011, pp. 15-27. https://doi.org/10.4018/978-1-60960-186-7.ch002

APA

Shasha, D. & Amos, M. (2011). DNA Hash Pooling and its Applications. In B. MacLennan (Ed.), Theoretical and Technological Advancements in Nanotechnology and Molecular Computation: Interdisciplinary Gains (pp. 15-27). IGI Global. https://doi.org/10.4018/978-1-60960-186-7.ch002

Chicago

Shasha, Dennis, and Martyn Amos. "DNA Hash Pooling and its Applications." In Theoretical and Technological Advancements in Nanotechnology and Molecular Computation: Interdisciplinary Gains, edited by Bruce MacLennan, 15-27. Hershey, PA: IGI Global, 2011. https://doi.org/10.4018/978-1-60960-186-7.ch002

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Abstract

In this article we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning, which can prove costly and time consuming, even with current sequencing techniques. Our overall objective is to address issues such as whole genome detection, fragment detection and sample similarity. Because our method is similar in spirit to hashing in computer science, we call it DNA hash pooling. To illustrate this method, we describe protocols using pairs of restriction enzymes. The in silico empirical results we present reflect a sensitivity to experimental error. Our method, performed as a filtering step prior to sequencing, may reduce the amount of sequencing required (generally by a factor of 10 or more). Even as sequencing becomes cheaper, an order of magnitude remains important.

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