Scripting Analyses of Genomes in Ensembl Plants

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2022 Jan 17

PMID 35037199

Authors

Bruno Contreras-Moreira

Guy Naamati

Marc Rosello

James E Allen

Sarah E Hunt

Matthieu Muffato

Astrid Gall

Paul Flicek

Affiliations

Soon will be listed here.

Abstract

Ensembl Plants ( http://plants.ensembl.org ) offers genome-scale information for plants, with four releases per year. As of release 47 (April 2020) it features 79 species and includes genome sequence, gene models, and functional annotation. Comparative analyses help reconstruct the evolutionary history of gene families, genomes, and components of polyploid genomes. Some species have gene expression baseline reports or variation across genotypes. While the data can be accessed through the Ensembl genome browser, here we review specifically how our plant genomes can be interrogated programmatically and the data downloaded in bulk. These access routes are generally consistent across Ensembl for other non-plant species, including plant pathogens, pests, and pollinators.

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