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
- 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