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

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How to ...

Download sequence from PlantGDB

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

To download raw sequence, go to Sequence->Download->Public Plant Sequence, and type the species name.
To download assemblies, go to Sequence->Download->EST Assemblies or ->GSS Assemblies, and click on the species of interest.
(Alternatively, use the FTP server: Go to Sequence->FTP Server->Download->FASTA_NNN (GenBank/UniProt where NNN is current version) or ->PUT (EST assemblies).)
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.

Find out what EST assemblies are available

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.

Use the batch BLAST tool at PlantGDB

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

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

Annotate a gene structure

Register for an account from a Genome Browser Home Page (example: AtGDB) -see upper left.
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.
Open yrGATE tool by clicking 'Annotate This Region!'. yrGATE displays gene models and evidence alignments along with tools for building a new annotation.
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.
Validate your gene model using web portal tools (ORF Finder, BLAST).
Enter Description and a unique ID for your annotation and click 'Submit' or 'Save' for later editing.
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.

Identify colinear regions in two or more genomes

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.

Public Plant Sequence Release 175

Species-parsed Viridiplantae sequences from GenBank and UniProt, available for search, download or BLAST.

More about Plant Sequence...

Version Release 175 (2009-12-20)

See below for totals by type. View example of a sequence record. View all sequence resources at PlantGDB.

Seq Type	Description	Species Count	Sequence Count
Protein	UniProt Protein	47,383	590,784
EST	Expressed Sequence Tag	725	20,968,343
GSS	Genome Survey Sequence	290	10,898,757
STS	Sequence Tagged Sites	266	153,310
HTG	High Throughput Genomic DNA	65	24,496
HTC	High Throughtput cDNA	104	62,154
PLN	PLN Division mRNA	89,337	1,277,697
DNA_PLN	PLN Division DNA	88,877	905,537

Sequence Assemblies

PlantGDB-assembled unique transcripts (PUT) and Genome Survey Sequence assemblies (GSS), available for search, download or blast.

More about Assemblies...

Tools

Online tools for pattern matching, sequence query, and spliced alignment.

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
FindPrimers	A tool for designing PCR primers for analyzing maize Ds transposon insertions.
GeneSeqer Parallel 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

BioExtract Server provides powerful database queries, analysis tools, and online workflows.

More about Workflows...

Genome Browsers

17 genome browsers for emerging & complete plant genomes, featuring high quality spliced-alignment of transcripts/proteins and gene structure annotation. (Video: QuickTime Flash )

More about Genome Browsers...

Genome Databases at PlantGDB

GDB	Species	Type	Assembly	GeneModels
AtGDB	Arabidopsis thaliana	Chromosome	TAIR9	TAIR9
BdGDB	Brachypodium distachyon	Chromosome	Version 1.0	Brachy1.0
BrGDB	Brassica rapa	BAC	n/a	GenBank
CpGDB	Carica papaya	Scaffold	GenBank	GenBank
GhGDB	Gossypium hirsutum	BAC	n/a	GenBank
GmGDB (Chr)	Glycine max	Chromosome	Glyma1	Glyma1
GmGDB (BAC/Scaf)	Glycine max	BAC/Scaffold	Glyma0/Gbk	Glyma0.1b
HvGDB	Hordeum vulgare	BAC	n/a	GenBank
LjGDB	Lotus japonicus	Chromosome	Lj1.0	Lj1.0
MtGDB	Medicago truncatula	Chromosome	Mt2.0	Mt2.0
OsGDB	Oryza sativa	Chromosome	Release 6.1	Release 6.1
PpGDB	Physcomitrella patens	Scaffold	Phypa1.1	Phypa1.1
PtGDB	Populus trichocarpa	Chromosome	Poptr1	Poptr1.1
SbGDB	Sorghum bicolor	Chromosome	Sbi1	Sbi1.4
SlGDB	Solanum lycopersicum	BAC	n/a	GenBank
TaGDB	Triticum aestivum	BAC	n/a	GenBank
VvGDB	Vitis vinifera	Chromosome	Genoscope	Genoscope
ZmGDB (Chr)	Zea mays	Chromosome	n/a	4a.53 filtered
ZxGDB (BAC/Scaf)	Zea mays	BAC	n/a	GenBank

Community Annotation

Online tools and resources for gene structure annotation. Community-contributed annotations can be viewed at PlantGDB or remotely (Video: QuickTime Flash )

More about Community Annotation...

Special Datasets

Special datasets for transposon insertion sites, splicing-related genes, and more.

More about Special Datasets...

Dataset	Description
AcDs Tagging	AcDs transposon tagging of maize
ASIP	Alternative Splicing in Plants
PLEXdb	Gene Expression Database
RescueMu	RescueMu-tagged GSS sequences are generated by Maize Gene Discovery Project. Sequences matching GSS contigs have been annotated
SRGD	A searchable database of splicing related genes
UniformMu	MuTAIL sequences are generated by UniformMu transposon. Sequences matching GSS contigs have been annotated and are available for download

Outreach

Plant Genome Research Outreach Portal (PGROP) for locating activities, programs and resources; Outreach Program for Native Americans.

What's New?

Click below or view all news
Latest update: January 20, 2010

Transcript Assembly Update

New and refreshed transcript assemblies (PUTs) based on GenBank Release 175 are available for download and BLAST at PlantGDB.
New PUT assemblies include:

Fragaria x ananassa (garden strawberry)
Jatropha curcas (Barbados nut)
Mimulus guttatus var. nasutus (common monkeyflower)
Mimulus lewisii (purple monkeyflower)
Phyllostachys edulis (tortoiseshell bamboo)
Pisum sativum (garden pea)
Pinus contorta (lodgepole pine)
Quercus petraea (sessile oak).
Quercus robur (English oak)
Solanum melongena (eggplant)
Solanum torvum (turkeyberry)

Refreshed assemblies include:

Brachypodium distachyon (Brachypodium)
Bruguiera gymnorhiza (large-leafed mangrove)
Cicer arietinum (chickpea)
Coffea arabica (coffee)
Cucumis sativus (cucumber)
Festuca arundinacea (tall fescue)
Musa acuminata (banana)
Picea abies (Norway spruce)
Picea glauca (white spruce)
Phaseolus coccineus (scarlet runner bean)
Picea sitchensis (Sitka spruce)
Solanum habrochaites (wild tomato)
Solanum pennellii (wild tomato)

View all PUT assemblies on our EST Assembly Data Page. (January 21, 2010)

GenBank Release 175

GenBank Release 175.0 sequence data are now available on our Download Page. PUT assemblies are currently being updated (January 15, 2010).

New Help Links

Need help understanding what you see on a page? Click the help icon,

, for a popup explanation and additional resources. We will be rolling this system out across PlantGDB soon; for now, it's implemented for Genome Browsers (Example).

Links to CIWOG

CIWOGPlants is a database of common introns from 29,967 orthologous gene clusters from eight plant species*. PlantGDB now links to CIWOG alignments: from the gene model record page (see example), click on the @ CIWOG (loose) link under "Additional Resource Links" to search the CIWOG database for this gene model (January 6, 2010)
*Briefings in Bioinformatics 10:631 (2009) (abstract)

Genome browser video

A new 6 minute video tutorial, "How to use genome browsers at PlantGDB", is available from the Home page, Help & Tutorials, or any Genome browser page (December 26, 2009).

Parallel GeneSeqer

GeneSeqer has been installed on USD's high performance computer system, and a Parallel GeneSeqer web interface is available for larger runs (December 26, 2009).

PtGDB (Populus trichocarpa) update

PlantGDB's genome browser for Populus trichocarpa (PtGDB) has been updated to incoporate JGI poptr v1.1 gene model annotations and up-to-date PlantGDB spliced alignments to cDNA, EST, and related species proteins (December 10, 2009).

Annotation video

Check out the new gene structure annotation video, available from Help and Tutorials page or any genome browser. This 4.5 minute video demonstrates the yrGATE annotation tool in action (December 2, 2009).

Maize genome annotation

Community-annotated maize gene models at ZmGDB (see an example) can now be viewed at MaizeGDB and maizesequence, by means of Distributed Annotation Service (DAS). (November 20, 2009).

What's Coming?

Manihot esculenta (cassava) genome browser: The recently-released Manihot esculenta draft genome consists of 11,243 scaffolds spanning 416Mb. PlantGDB will release a cassava genome browser incorporating EST, cDNA, PUT and related-species protein alignments as well as published gene models (expected Jamuary, 2010).

PlantGDB

Sequence

Genomes

Tools

Datasets

Outreach

Help

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

Public Plant Sequence Release 175

Version Release 175 (2009-12-20)

Sequence Assemblies

PUT Assemblies

GSS Assemblies

Tools

Workflow Management

Genome Browsers

Genome Databases at PlantGDB

Community Annotation

Special Datasets

Outreach

What's New?

What's Coming?

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