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

Methods Mol Biol. 2016;1374:115-40. doi: 10.1007/978-1-4939-3167-5_6.

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 ).

Keywords: Cereals; Comparative genomic s; Crops; Databases; Functional genomic s; Genetic variation; Genome browser; Genomics; Phenotype; Transcriptomics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Data Mining / methods
  • Databases, Genetic
  • Genome, Plant
  • Genomics / methods*
  • Plants / genetics*
  • Web Browser