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

  • Dan BolserEmail author
  • Daniel M. Staines
  • Emily Pritchard
  • Paul Kersey
Part of the Methods in Molecular Biology book series (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).

Key words

Databases Genomebrowser Genomics Transcriptomics Functional genomics Comparative genomics Geneticvariation Phenotype Crops Cereals 

Notes

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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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Dan Bolser
    • 1
    Email author
  • Daniel M. Staines
    • 1
  • Emily Pritchard
    • 1
  • Paul Kersey
    • 1
  1. 1.European Molecular Biology LaboratoryEuropean Bioinformatics InstituteHinxton, CambridgeUK

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