Welcome to plantgdb.org!Tools and resources for plant genomics

PlantGDB provides species-parsed sequence from GenBank and UniProt, as well as custom EST/GSS assemblies, for batch download or search.

1. To download raw sequence, go to Sequence->Download->Public Plant Sequence, and type the species name.
2. To download assemblies, go to Sequence->Download->EST Assemblies or ->GSS Assemblies, and click on the species of interest.
3. (Alternatively, use the FTP server: Go to Sequence->FTP Server->Download->FASTA_NNN (GenBank/UniProt where NNN is current version) or ->PUT (EST assemblies).)
4. To search on ID keyword, go to Sequence->Search->ID or Keyword Search, and enter an ID keyword in the search box.

For more information see Search Overview page.

Go to Sequence->EST Assemblies, and click 'View Current Assemblies' to see a table of assemblies currently available. You can then click an organism name to access a download page for all assembly-related sequence files.

The BLAST tool allows batch queries against plant species, taxonomic groups, and special datasets:

1. Go to Tools->Blast
2. To query a taxonomic group or other dataset, select a preset (e.g. "All Grasses"; "Maize BACs")
3. To query a species, begin typing the desired genus/species in the "Species Name" box and click to select the correct species.
4. You may combine any number of species and groups in your BLAST query.
5. Then paste up to 100 FASTA formatted sequences or sequence IDs in the query window, select an algorithm and parameter settings, and click 'Execute'.

1. Register for an account from a Genome Browser Home Page (example: AtGDB) -see upper left.
2. Enter the ID for a gene you want to annotate in the Search window (example: At1g01010.1). Then click 'Search: Genome'. The result is a Genome Context view of that gene.
3. Open yrGATE tool by clicking 'Annotate This Region!'. yrGATE displays gene models and evidence alignments along with tools for building a new annotation.
4. Build a gene model by clicking exons or exon coordinates. The new gene model is displayed in green as "Your Structure", and the resulting sequence is displayed in the mRNA window.
5. Validate your gene model using web portal tools (ORF Finder, BLAST).
6. Enter Description and a unique ID for your annotation and click 'Submit' or 'Save' for later editing.
7. PlantGDB will email you when your annotation is approved or rejected. Once approved, your annotation and its evidence can be viewed in a Genome Browser and is available for remote display through DAS.

For more details, check out the tutorials and video demos on our Help and Tutorials pages.

PlantGDB's genome browsers provide links to the GEvo tool for viewing genome colinearity, part of the CoGe genome website. For details, see Genome Browser Help.