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Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data

  • Protocol
Plant Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1374))

Abstract

Ensembl Plants (http://plants.ensembl.org) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.

Ensembl Plants is updated 4–5 times a year and is developed in collaboration with our international partners in the Gramene (http://www.gramene.org) and transPLANT projects (http://www.transplantdb.org).

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Acknowledgements

“The transPLANT project is funded by the European Commission within its 7th Framework Programme, under the thematic area “Infrastructures”, contract number 283496”.

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Authors and Affiliations

  1. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

    Dan Bolser, Daniel M. Staines, Emily Pritchard & Paul Kersey

Authors
  1. Dan Bolser
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  2. Daniel M. Staines
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  3. Emily Pritchard
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  4. Paul Kersey
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Corresponding author

Correspondence to Dan Bolser .

Editor information

Editors and Affiliations

  1. School of Plant Biology, University of Western Australia, Perth, Australia

    David Edwards

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Bolser, D., Staines, D.M., Pritchard, E., Kersey, P. (2016). Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data. In: Edwards, D. (eds) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3167-5_6

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  • DOI: https://doi.org/10.1007/978-1-4939-3167-5_6

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3166-8

  • Online ISBN: 978-1-4939-3167-5

  • eBook Packages: Springer Protocols

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