A Brief Tour of PlantGDB!

Click on a topic to view a brief description and site navigation links and tips.

PlantGDB is a genomics database encompassing green plant (Viridiplantae) sequence data.

  • Users can search, BLAST, or download nucleotide or protein sequences from over 70,000 species as well as access custom transcript assemblies for over 200 species.
  • Sixteen plant genome browsers (xGDB) are available, with a focus on accurate spliced-alignment of transcript and protein.
  • PlantGDB provides web tools for sequence analysis and a unique bioinformatics workflow environment (BioExtract).
  • PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.
  • PlantGDB downloads all plant sequence from GenBank approximately every 4 months, parses it by species, and makes it available for download, search, and BLAST analysis. Advanced sequence search capabilities are provided using TableMaker (See below).
    • To get there: Sequence > Public Plant Seq > Species Search or Keyword/ID Search
  • PlantGDB also provides custom transcript assemblies (PUTs or PlantGDB-derived Unique Transcripts) for all plant species with >10,000 ESTs, or by special request. Users can download PUT datasets, perform batch BLAST, or do keyword searches based on GO annotations and top Uniprot BLAST hits.
    • To get there: Sequence > EST Assembly
  • Genome Survey Sequence (GSS) assemblies are provided for maize and sorghum.
    • To get there: Sequence > GSS Assembly
  • Sequence Overview
  • PlantGDB provides genome browsers for sixteen plant species (chromosome, scaffold, or BAC-based). Each genome assembly is splice-aligned to transcripts as well as protein from similar species and presented in a simple graphical interface (the xGDB platform). An important feature of xGDB is the ability to view spliced alignment data for all aligned sequences.
  • Powerful search tools are provided for finding sequences and retrieving sequence data adjacent to coding regions, as well as BLAST and GeneSeqer. DAS (Distributed Annotation Service) is available for both viewing (DAS client) and exporting (DAS server) genome-aligned sequence. Finally, each genome browser has tools for community annotation of genes, as a way to improve the quality of gene models.
    • To get there: Genomes > (select GDB)
  • Genome Browser Overview | Help Page
  • Accurate and complete gene models (annotations) are essential to understanding genome biology. PlantGDB's yrGATE tool harnesses the power of the community to create gene annotations right in a xGDB genome browser. The tool shows all splice junctions revealed by transcript evidence and allows the user to easily create and validate gene models with a just few mouse clicks. Registered users can submit annotation for curation at PlantGDB.
  • After a submitted annotation is approved by the PlantGDB administrator, it is incorporated into the genome browser and is publicly viewable on the yrGATE track. To help identify genes most in need of annotation, the GAEVAL tool classifies potentially mis-annotated genes and displays them in tabular format.
    • To get there: Genomes > (select genome) > Login or Register
  • Annotation Overview | Help Page

PlantGDB provides special datasets for search and download:

  • SRGD, a Splice-Related Gene Database, in which splicing-related genes are compiled for model system species (animal and plant). To get there: Datasets > SRGD
  • ASIP, Alternative Splicing in Plants, a database encompassing alternative splicing in Arabidopsis, rice, Medicago truncatula and Lotus japonicus. To get there: Datasets > ASIP
  • Ac/Ds Transposons in maize, a project to tag maize genes using Ds. View tagged loci using BLAST or ZmGDB genome browser; order seed from tagged accessions To get there: Datasets > Ac/Ds Tagging;
  • RescueMu and Uniform Mu datasets, cataloging tagged GSS sequences. To get there: Datasets > RescueMu or UniformMu

Datasets Overview

  • PlantGDB provides a variety of tools for sequence analysis including BLAST, GeneSeqer Spliced Alignment, GenomeThreader Spliced Alignment, MuSeqBox, PatternSearch, Tracembler, and TE nest.
    • To get there: Tools > Overview or (select tool)
  • see below for more details on two additional tools at PlantGDB: TableMaker, a sequence database query tool, and BioExtract, a website for creating and executing custom informatics queries and workflows.
  • Tools Overview
  • TableMaker is an online search tool that queries GenBank tables housed at PlantGDB using MySQL queries constructed in an easy-to use GUI environment.
    • To get there: Tools > TableMaker
  • TableMaker | Help Page
  • The BioExtract Server provides a Web interface for automating bioinformatics workflows. In a single environment, users can query sequence databases, analyze data with Web-based or local bioinformatics tools, save results, and create and manage workflows.
  • As a simple example, a user could develop a workflow that performs a BLAST search, retrieves peptide sequences from query results, eliminates redundant sequences, and produces a multiple sequence alignment output. BioExtract workflows can be paused, modified, saved, shared with an online workgroup or the world, and documented electronically for future reference.
    • To get there: Tools > BioExtract
  • BioExtract Server
  • PlantGDB's PGROP (Plant Genome Research Outreach Portal) site provides a centralized access point for locating Plant Genome Research "Outreach" activities, programs and resources.
    • To get there: Outreach > PGROP
  • PGROP


New & Noteworthy

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New Location for PlantGDB (July 23, 2012)
The Brendel Group is now located at Indiana University, and the PlangGDB server has been migrated as well, and it is now hosted at the Indiana University School of Informatics and Computing. We don't anticipate any disruption in service, but if you encounter any problems with the website we encourage you to contact us using our Feedback Form. (3-14-2012)
BrGDB - Brassica rapa chromosome-based genome browser (Mar. 16)
StGDB - Solanum tuberosum new genome browser (Mar. 16)
StGDB, a new genome database for the potato (Solanum tuberosum) is now available at PlantGDB (Genomes→Other→StGDB). Based on the JGI draft genome, VcGDB includes 14,971 protein-coding loci and 15,285 protein-coding transcripts on 413 scaffolds. Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-14-2012)
BrGDB - Brassica rapa chromosome-based genome browser (Mar. 16)
BrGDB, the genome browser for rapeseed (Brassica rapa) is now updated at PlantGDB (Genomes→Other→BrGDB). Based on the BRAD draft genome, BrGDB includes 41,019 protein-coding transcripts on 10 chromosomes plus unanchored scaffolds (concatenated with 200 N spacer as "chr11"). Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-16-2012)
VcGDB - Volvox carteri new genome browser (Mar. 14)
VcGDB, a new genome database for the multicellular green alga Volvox (Volvox carteri) is now available at PlantGDB (Genomes→Other→VcGDB). Based on the JGI draft genome, VcGDB includes 14,971 protein-coding loci and 15,285 protein-coding transcripts on 413 scaffolds. Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (3-14-2012)
Medicago genome updated (Feb 27)
The Medicago truncatula (barrel medic) genome browser MtGDB has been updated to the new assembly / annotation version 3.5 using data deposited at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Rice genome updated (Feb 27)
The Oryza sativa (rice) genome browser OsGDB has been updated to the new assembly / annotation version 7 using data deposited at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Cassava genome updated (Feb 27)
The Manihot esculenta (cassava) genome browser MeGDB has been updated to the v4 assembly / v4.1 annotation that is available at phytozome. New transcript / protein spliced alignments and gene quality estimates have been calculated as well.
Populus annotation updated (Feb 27)
The Populus trichocarpa (poplar) genome browser PtGDB has been updated to annotation version 2.2 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Mimulus annotation updated (Feb 27)
The Mimulus guttatus genome browser MgGDB has been updated to annotation version 4.3 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Chlamydomonas annotation updated (Feb 27)
The Chlamydomonas reinhardtii genome browser CrGDB has been updated to annotation version 4.3 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
Brachopodium annotation updated (Feb 13)
The Brachypodium distachyon genome browser BdGDB has been updated to annotation version Bradi1.2 using data deposited at phytozome. Genome assembly and spliced-alignments are unchanged.
PlantGDB NSF Grant (Jan 31)

The PlantGDB website is currently being managed under a new NSF Genome Research Grant, IOS-1126267 (IPGA: Characterization, Modeling, Prediction, and Visualization of the Plant Transcriptome.) Read more about IPGA.

PlantGDB at Maize Genetics Conf. (Jan 31)
PlantGDB will be represented at the 54th Annual Maize Genetics Conference, March 15-18, 2012, in Portland, Oregon USA. Check out poster P56 "Discovery, annotation and expression analysis of arginine/serine (SR) proteins in maize using the Plant Genome Database PlantGDB". (1-28-2012)
GenBank Release 187 (Jan 31)
GenBank Release 187.0 sequence data (close date 12-15-2011) have been processed and are available for downloading at PlantGDB. Twenty-three new or updated transcript assemblies have been created. Please note that indexing the new sequence data has been postponed due to infrastructure issues. (2-27-2012)
New Add Track feature for Genome Browsers Dec 15
Users can add their own genome features (aligned transcripts, gene models, etc) using our User Add Track tool. All that's needed is a properly formatted gff3 file. This feature is currently available at ZmGDB and AtGDB/ and will be available soon for all GDB. (12-15-2011).

What's Coming?

Genome updates (1-31-2012)
We are in the process of prioritizing genomes at PlantGDB for update. In addition, newly-available plant genomes are being prioritized for inclusion in PlantGDB's Genome Browser suite. Our goal is to maintain current data for at least 25 genomes.

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