Welcome to www.plantgdb.org! Tools and resources for plant genomics.
Returning visitors, note the changes since your last visit on the right, or on our News page.
First time visitors: we've got a brief tour of PlantGDB that shows how to use our site.
If you experience issues using our site with Internet Explorer, please see our Web Browser Support page.
Features:
Public Plant Sequence
All plant sequences from GenBank and UniProt, parsed by species and available for searching or download (view an example). Updated Transcript Assemblies (v.171).
GenBank Release 171 (2009-04-15).
Sequence Assemblies
Custom transcript assemblies (PUT) for
192 species (view an example) as well as GSS assemblies for maize and sorghum. The most current assemblies are version:
171a
Web Tools
Online tools for pattern matching and spliced alignment, as well as specialized sequence query tools.
More about Tools...
| Tool | Description |
|---|---|
| BioExtract Server | An online service for creating and customizing bioinformatics workflows |
| BLAST | An NCBI-BLAST service with , species-parsed plant databases and batch query capabilities |
| DAS | Distributed Annotation System (DAS) allows remote genome browsers to access PlantGDB annotations |
| GeneSeqer | A tool for generating gene models based on transcript - genome spliced alignment |
| GenomeThreader | A tool for generating gene models based on transcript or protein:genome spliced alignment |
| MuSeqBox | A program that tabulates BLAST output and filter hits according to user-specified criteria |
| PatternSearch | A tool for querying short sequences (e.g. PCR fragments) for genome homology |
| ProbeMatch | Query your sequence against microarray probe sequences |
| TableMaker | Search PlantGDB's Plant Sequence database with an easy-to use GUI interface. |
| TE_Nest | An annotation and visualization tool for the identification transposable elements in genomic sequence |
| TracEmbler | Perform chromosome walks based on a query sequence, using trace sequences from NCBI's Trace Archive. |
| yrGATE | A tool for community annotation of genomic sequence, used in conjunction with the xGDB genome browsers |
Workflow Management
PlantGDB's BioExtract Server provides powerful database queries, sequence analysis tools, and the ability to create and manage workflows online .
Genome Browsers
Featuring high quality spliced alignments to transcripts / proteins and gene models, for 16 complete & emerging plant genomes (Overview).
Community Annotation
Online community annotation of emerging genomes, curated and published to the genome browser.
Special Datasets
Special datasets are available for transposon insertion sites, splicing-related genes, and more. Updated AcDs Tagging dataset for maize
Outreach
Plant Genome Research Outreach Portal (PGROP), a centralized access point for locating Plant Genome Research "Outreach" activities, programs and resources.