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Design of an Enterobacteriaceae Pan-Genome Microarray Chip

  • Conference paper
Computational Systems-Biology and Bioinformatics (CSBio 2010)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 115))

Abstract

Microarrays are a common method for evaluating genomic content of bacterial species and comparing unsequenced bacterial genomes. This technology allows for quick scans of characteristic genes and chromosomal regions, and to search for indications of horizontal transfer. A high-density microarray chip has been designed, using 116 Enterobacteriaceae genome sequences, taking into account the enteric pan-genome. Probes for the microarray were checked in silico and performance of the chip, based on experimental strains from four different genera, demonstrate a relatively high ability to distinguish those strains on genus, species, and pathotype/serovar levels. Additionally, the microarray performed well when investigating which genes were found in a given strain of interest. The Enterobacteriaceae pan-genome microarray, based on 116 genomes, provides a valuable tool for determination of the genetic makeup of unknown strains within this bacterial family and can introduce insights into phylogenetic relationships.

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Author information

Authors and Affiliations

  1. Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, 2800, Kongens Lyngby, Denmark

    Oksana Lukjancenko & David W. Ussery

Authors
  1. Oksana Lukjancenko
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  2. David W. Ussery
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Editor information

Editors and Affiliations

  1. School of Information Technology, King Mongkut’s University of Technology Thonburi, 126 Pracha U-Thit Rd, Bangmod, Thungkru, 10140, Bangkok, Thailand

    Jonathan H. Chan

  2. School of Computer Engineering, Nanyang Technological University, Block N4, 2b-39,Nanyang Avenue, 639798, Singapore

    Yew-Soon Ong

  3. Dept. of Computer Science, Yonsei University, 134 Shinchon-dong, Sudaemoon-ku, 120-749, Seoul, South Korea

    Sung-Bae Cho

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Lukjancenko, O., Ussery, D.W. (2010). Design of an Enterobacteriaceae Pan-Genome Microarray Chip. In: Chan, J.H., Ong, YS., Cho, SB. (eds) Computational Systems-Biology and Bioinformatics. CSBio 2010. Communications in Computer and Information Science, vol 115. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-16750-8_15

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  • DOI: https://doi.org/10.1007/978-3-642-16750-8_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-16749-2

  • Online ISBN: 978-3-642-16750-8

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