Databases

Overview

This page has links to databases for sequences, tools, workflows and plants.
Some of these databases are for one plant species only; some are for a selection of species with tools to compare genome features.
Most of these databases are linked to at least one other database by inputs or outputs.
Databases are sometimes abandoned - look at the most recent update/release or news on the start page to find out if it is current. The ones in the links below seem to be active.
There is no single standard repository for annotated genomes: these are held across various databases.

NCBI: Sequence Read Archive: https://www.ncbi.nlm.nih.gov/sra
NCBI: Genomes: https://www.ncbi.nlm.nih.gov/home/genomes/
NCBI: RefSeq: https://www.ncbi.nlm.nih.gov/refseq/
European Nucleotide Archive: (a mirror of NCBI but with different search options): https://www.ebi.ac.uk/ena
Protein Databank: https://www.rcsb.org/
UniProt: protein sequences: https://www.uniprot.org/
Ensembl Plants: https://plants.ensembl.org/index.html
JGI Phytozome: https://phytozome.jgi.doe.gov/pz/portal.html
UCSC Genome Browser: https://genome.ucsc.edu/index.html
TAIR - Arabidopsis thaliana: https://www.arabidopsis.org/
Genome database for Rosaceae: https://www.rosaceae.org/
Gramene - crops and model plant species: http://gramene.org/
PlaBiPD - includes a chronology and phylogeny of pubplished plant genomes: https://plabipd.de/index.ep
PLAZA: https://bioinformatics.psb.ugent.be/plaza/