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DNA Chips for Species Identification and Biological Phylogenies

  • Conference paper
DNA Computing and Molecular Programming (DNA 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5877))

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Abstract

The codeword design problem is an important problem in DNA computing and its applications. Several theoretical analyses as well as practical solutions for short oligonucleotides (up to 20-mers) have been generated recently. These solutions have, in turn, suggested new applications to DNA-based indexing and natural language processing, in addition to the obvious applications to the problems of reliability and scalability that generated them. Here we continue the exploration of this type of DNA-based indexing for biological applications and show that DNA noncrosshybridizing (nxh) sets can be successfully applied to infer ab initio phylogenetic trees by providing a way to measure distances among different genomes indexed by sets of short oligonucleotides selected so as to minimize crosshybridization. These phylogenies are solidly established and well accepted in biology. The new technique is much more effective in terms of signal-to-noise ratio, cost and time than current methods. Second, it can be scaled up to newly available universal DNA chips readily available both in vitro and in silico. In particular, we show how a recently obtained such set of nxh 16-mers can be used as a universal coordinate system in DNA spaces to characterize very large groups (families, genera, and even phylla) of organisms on a uniform reference system, a veritable and comprehensive “Atlas of Life”, as it is or as it could be on earth.

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Author information

Authors and Affiliations

  1. Biology, Computer Science, The University of Memphis, Tennessee, 38152

    Max H. Garzon, Tit-Yee Wong & Vinhthuy Phan

Authors
  1. Max H. Garzon
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  2. Tit-Yee Wong
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  3. Vinhthuy Phan
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Editor information

Editors and Affiliations

  1. Dept. of Computer Science and Computer Engineering, JBHT - CSCE 504, 1 University of Arkansas, 72701, Fayetteville, AR, USA

    Russell Deaton

  2. Department of Life Science and Institute of Physics Graduate school of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, 153-8902, Tokyo, Japan

    Akira Suyama

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Garzon, M.H., Wong, TY., Phan, V. (2009). DNA Chips for Species Identification and Biological Phylogenies. In: Deaton, R., Suyama, A. (eds) DNA Computing and Molecular Programming. DNA 2009. Lecture Notes in Computer Science, vol 5877. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-10604-0_6

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  • DOI: https://doi.org/10.1007/978-3-642-10604-0_6

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-10603-3

  • Online ISBN: 978-3-642-10604-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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