PlantGDB

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About PlantGDB and Genome Annotation

Update, 01-July-2015: The plantgdb.org web resource was managed most recently under NSF-funded project (IOS-1221984). This grant has now ended, and the PlantGDB website is no longer being updated. However, you can check out another Brendel Lab project, xGDBvm, a virtual environment for genome annotation. xGDBvm instances are currently available to registered users of iPlant Atmosphere

Previously, PlantGDB was developed under NSF grants IOS-0606909 and DBI-0110254 and DBI-0321600.

Project Objectives

The scale of sequence and other data accumulation in plant genomics is outstripping our ability effectively to annotate those genomes. The goal of this project is to develop novel, highly automated, scalable, comprehensive, and accurate approaches to genome annotation to address this problem. Project deliverables include (1) software that implements the novel prediction algorithms, (2) visualization and data access portals, and (3) a cyberinfrastructure environment implementation of the developed tools for distributed computing, sharing of protocols, and analysis provenance recording. In the long run, the project seeks to explore the extent to which genomic biology can transition from a largely descriptive to a highly predictive science driven by quantitative measurements, with algorithms and computation as the domain-adapted language. Read more about project goals and approaches.

Outreach

Discovery, annotation and expression analysis of arginine/serine (SR) proteins in maize using the Plant Genome Database PlantGDB. See poster P56, 2012 Maize Genetics Conference for a synopsis of progress to date.

Learn More:

The links below provide more information about PlantGDB and related topics (see also left menu):

News - View recent and old PlantGDB announcements
Tour- A brief tour through PlantGDB.org
F.A.Q. - Frequently Asked Questions
Site Map - Heirarchical map of PlantGDB.org
Publications associated with PlantGDB
Links relevant to plant genomes and plant sequence data
Acknowledgments - Funding and contributors to PlantGDB

Get Help:

Help/Tutorials - Help Pages and Tutorials covering major PlantGDB resources and tools

How to Contact PlantGDB

The easiest way to contact us is with the Feedback link in the top menu area, accessible from ANY PlantGDB page. We will do our best to get back to you within 24 hours.

If you wish to contact the PlantGDB website manager or one of the Project PI's, institution links and email addresses are listed below.

PlantGDB Website & Database Manager: Dr. Jon Duvick, jduvick@iastate.edu
Project PI: Dr. Volker Brendel, vbrendel@indiana.edu
Co-PI: Dr. Karin Dorman, kdorman@iastate.edu
Co-PI: Dr. Shailesh Lal, lal@oakland.edu
Senior Personnel: Dr. Yasser El-Manzalawy, yasser@iastate.edu
PlantGDB Questions/Comments: plantgdb-l@list.indiana.edu

Thanks for visiting, and we look forward to hearing from you!

New & Noteworthy

Click below or view all news | Twitter

What comes after PlantGDB? (July 1, 2015): PlantGDB's NSF funding has ended and the website is no longer being updated. However, you can check out a related project from the Brendel Lab, xGDBvm, a virtual environment for genome annotation in the cloud. xGDBvm instances are now available to registered users of iPlant Atmosphere (3-14-2012)
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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2012): 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, 2011: 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.