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. 2017:1533:1-31.
doi: 10.1007/978-1-4939-6658-5_1.

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

Dan M Bolser  1 , Daniel M Staines  2 , Emily Perry  2 , Paul J Kersey  2
Affiliations

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

Dan M Bolser et al. Methods Mol Biol. 2017.

Abstract

Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for 39 sequenced plant species. Available data includes genome sequence, gene models, functional annotation, and polymorphic loci; for the latter, additional information including population structure, individual genotypes, linkage, and phenotype data is available for some species. Comparative data is also available, including genomic alignments and "gene trees," which show the inferred evolutionary history of each gene family represented in the resource. Access to the data is provided through a genome browser, which incorporates many specialist interfaces for different data types, through a variety of programmatic interfaces, and via a specialist data mining tool supporting rapid filtering and retrieval of bulk data. Genomic data from many non-plant species, including those of plant pathogens, pests, and pollinators, is also available via the same interfaces through other divisions of Ensembl.Ensembl Plants is updated 4-6 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.eu ).

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

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