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Plant Genomics Databases pp 173–181Cite as

Species-Specific Genome Sequence Databases: A Practical Review

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1533))

Abstract

This chapter presents a use case illustrating the search for homologues of a known protein in species-specific genome sequence databases. The results from different species-specific resources are compared to each other and to results obtained from a more general genome sequence database (Phytozome). Various options and settings relevant when searching these databases are discussed. For example, it is shown how the choice of reference sequence set in a given database influences the results one obtains. The provided examples illustrate some problems and pitfalls related to interpreting results obtained from species-specific genome sequence databases.

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Author information

Authors and Affiliations

  1. Applied Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

    A. D. J. van Dijk

  2. Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

    A. D. J. van Dijk

  3. Biometris, Plant Sciences Group, Wageningen University & Research Centre (WUR), Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands

    A. D. J. van Dijk

Authors
  1. A. D. J. van Dijk
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Correspondence to A. D. J. van Dijk .

Editor information

Editors and Affiliations

  1. PRI Bioscience, Biometris and Bioinformatics, Wageningen University & Research Wageningen, Wageningen, The Netherlands

    Aalt D.J van Dijk

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van Dijk, A.D.J. (2017). Species-Specific Genome Sequence Databases: A Practical Review. In: van Dijk, A. (eds) Plant Genomics Databases. Methods in Molecular Biology, vol 1533. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6658-5_9

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  • DOI: https://doi.org/10.1007/978-1-4939-6658-5_9

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6656-1

  • Online ISBN: 978-1-4939-6658-5

  • eBook Packages: Springer Protocols

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