An Updated Round-Up of the Top Plant Genome Databases
Posted 29th August 2018 by Kate Barlow
There’s more plant genome databases than there ever has been before. We’ve collated the most recent databases for ontology information on a variety of crops, including: rice, maize, wheat, sorghum, barley, millet, rye, and oats.
PlantGDB provides genome browsers that display current gene structure models and transcript evidence from spliced alignments of EST and cDNA sequences for Viridiplantae.
The FLAGdb++ is an integrative database that enables users to search and visualise data for high-throughput functional analysis of Arabidopsis, rice, and other plant genomes.
It has a user-friendly interface and incorporates hierarchical organisation of the data.
The running integration involves the structural and functional international annotations, ESTs from different plant species, novel gene predictions, mutant tags, gene families, protein motifs, transcriptome data, repeat sequences, primers and tags for genomic approaches, subcellular targeting, secondary structures, 3D models, MPSS tags, curated annotations and mutant phenotypes.
It is a genome-centric portal for plants of scientific interest, providing statistics and information on assembly, annotation, regulation, variation and sequences. Data can be searched by gene identifier or by BLAST sequence search.
Araport’s JBrowse allows you to explore DNA sequences graphically with a horizontal axis and scroll bar. You can also zoom in to view the nucleotide sequence and when zoomed out, it displays gene models, such as exons and introns. It also displays histograms of number of features per unit length.
Upon completion of the Oryza sativa ssp. japonica cv. genome sequencing by the International Rice Genome Sequencing Project, the The Rice Annotation Project established GBrowse with the aim to provide the scientific community with an accurate annotation of the rice genome sequence.
The Plant Genome and Systems Biology group focuses on the analysis of plant genomes, using bioinformatic techniques. To store and manage the data, they have developed PlantsDB – a database that stores data for individual plant species and provides a platform for integrative and comparative plant genome research.
Phytozome is a plant comparative genomics portal that provides a visual analysis of JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere, and facilitates accurate and insightful comparative genomics studies.
A comparative resource for cereal genomics. With a focus on rice, Gramene has marker, maps, gene, proteins, QTL, literature, diversity, pathway and ontology information on rice, maize, wheat, sorghum, barley, millet, rye, oats and wild rice.
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