85 new Ds-flanking sequences (fDs) have been placed in the maize reference genome. Visit the Ac/Ds Tagging project pages to search by region or gene to identify transposon insertions close to a gene of interest.
(5-8-2011).
New Transcript Assemblies May 3
New and refreshed transcript assemblies (PUTs) based on GenBank Release 183.0 are now available from our EST Cluster page (May 3, 2011).
GenBank Release 183.0 sequence data (close date 4-11-2011) have been downloaded and processed at PlantGDB; new blast indices will be in place by early May. New PUT Assemblies based on Release 183 are also in progress.(4-28-2011)
"All GDB" Table Improved Apr. 20
The "All GDB" page listing genome browsers available at PlantGDB has been expanded to include links to most features and tools available for each genome.
(4-20-2011).
SbGDB (Sorghum bicolor) genome update Apr.20
SbGDB (Sorghum bicolor; sorghum), a chromosome-based genome database at PlantGDB, has been updated with new splice-aligned transcripts current as of GenBank Release 181.0. Genome assembly and annotation remain the same.
(4-20-2011)
"All Loci/Annotations" Feature Release Apr. 14
The "All Loci/Annotations" page presents an ordered list of published gene loci and their EST/cDNA coverage/quality, together with any community annotations at that locus. Users can search by quality, keyword or region to find loci to re-annotate. (See example for GmGDB.) From the Top Menu choose Genomes → [XxGDB], Left Menu → All Loci/Annotations. Also available are custom "project" filters to facilitate annotation of the most interesting genes. Contact us for more info on adding projects.
(4-14-2011).
PeGDB - Prunus (peach) new genome browser Apr. 14
PeGDB, a new genome database for peach (Prunus persica) is now available at PlantGDB (Genomes->Dicots->PeGDB). Based on the JGI draft genome, PeGDB includes 27864 protein-coding loci and 28702 protein-coding transcripts on 202 scaffolds.
Other data displayed include splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (4-14-2011)
CpGDB (Carica papaya) genome update Apr. 14
CpGDB (Carica payaya; papaya), a scaffold-based genome database at PlantGDB, has been updated with new gene model annotations from JGI and new splice-aligned transcripts current as of GenBank Release 181.0. Total of 27,796 transcripts; 27,332 protein-coding loci. Genome assembly remains the same.
(4-14-2011)
GmGDB - Glycine max (soybean) genome update Apr. 14
GmGDB, a genome database for soybean (Glycine max) has been updated to display new EST and cDNA alignments (GenBank Release 181). GmGDB is based on the JGI-released draft genome and displays 46,367 protein-coding loci and 55,787 protein-coding transcripts on 20 pseudochromosomes (plus unlinked scaffolds which are concatenated and displayed as "chr21") (4-14-2011)
PpGDB (Physcomitrella patens) genome update Mar. 29
PpGDB (Physcomitrella patens; spike moss), a scaffold-based genome database at PlantGDB, has been updated with new gene model annotations from cosmoss (downloaded from JGI). Total of 38,354 transcripts; 32,273 genes. Genome assembly and spliced alignments remain the same as before.
(3-29-2011)
All GDB BLAST Feature Mar. 22
Now BLAST any genome-aligned sequence, gene model or predicted protein from most genome browsers using our new multi-genome BLAST. From any Genome Context View or Alignment Record (example), select BLAST @ All GDB, and choose from multiple protein (CDS translation), transcript (transcript/CDS, EST, PUT) or genomic (chr, BAC, scaffold) datasets against which to BLAST your query sequence(3-22-2011)
ZmGDB version 181 Mar. 22
ZmGDB (Zea mays genome browser) has been updated to GenBank Release 181. Spliced-alignments were re-run for EST, cDNA, and TPA (updated to GenBank 181), and PUT; for totals see Data & Methods. Additional improvements include better repeat masking of the RefGen_v2 assembly, using maizesequence.org masking data. Repeat masked regions are included in a new track and are blast-able. Gene models remain at 5b.60 (3-22-2011)
PlantGDB at Maize Genetics Conference Mar. 22
PlantGDB presented two posters at the 53nd Annual Maize Genetics Conference, March 17-20, 2011, at St. Charles, Illinois USA. Check out posters P25 and P26 in the 2011 meeting program for details. (3-22-2011)
If you have a list of maize genes you would like assigned to a project, please contact us.
(2-28-2011)
Setaria, Cucumis, Chlamydomonas genomes Feb. 14
Three new genome databases are available at PlantGDB:
SiGD: Setaria italica (foxtail millet), a scaffold-based genome assembly from JGI
CsGDB: Cucumis sativus (cucumber), a scaffold-based genome assembly from JGI
CrGDB:Chlamydomonas reinhardtii (green algae), a chromosome-based genome assembly from JGI
(2-14-2011)
Maize Filtered Gene Set (5b.60) Feb. 10
The Filtered Gene Set (FGS) from maizesequence.org, representing the most probable set of gene models, is now displayed at ZmGDB in addition to the Working Gene Set (WGS). The Loci/Annotations table now shows FGS loci by default.
PlantGDB talk and poster: "AcDs Tagging at PlantGDB: a Web Resource for Insertional Mutagenesis in Maize Using Dissociation (Ds)"; California Room: 2:30 PM Monday January 17. Schedule; Abstract. Also, stop by and see us at the Plant Genome DB booth! (1-10-11)
GenBank Release 181
GenBank Release 181.0 sequence data (close date 12-14-2010) are now live at PlantGDB, except for BLAST indices which are still being built. Therefore, for the moment BLAST searches still use version 179 data. New PUT Assemblies are underway and will be ready in late January. Our repository now includes the TSA (Transcriptome Shotgun Assembly) data type which represents short read assemblies deposited in GenBank.(1-3-11)
The Arabidopsis thaliana genome browser AtGDB has been updated to include TAIR10 gene models. Genome and spliced alignments are unchanged from TAIR9.(1-3-11)
2010 news
ZmGDB "All Loci/Annotations"
The ZmGDB All Loci/Annotations page presents an ordered list of gene loci (release 5a.59 ) and their EST/cDNA coverage/quality, together with any community annotations at that locus. Users can search by keyword or region to find loci to re-annotate. We've also begun classifying loci according to "projects" e.g. Classical Maize Genes (from CoGePedia) and Splicing Related Proteins as an aid to annotators.(12-21-10)
AcDsTagging workshop registration
Online registration is open for an AcDs Tagging workshop to be held from June 19-24, 2011 at the Boyce Thompson Research Institute. The workshop will provide hands on training in genetic and molecular genetic techniques for Ds reverse genetics, in conjuction with online resources at PlantGDB.org. See Workshop Announcement for details. (12-1-10)
Maize RefGen_v2 genome browser
The maize genome browser ZmGDB has been updated to the RefGen_V2 pseudomolecule assembly of maize inbred B73, as well as a new gene model build (5a.59) from maizesequence.org. The new annotations are displayed along with splice-aligned maize ESTs, cDNAs, PUT assemblies, and related-species proteins. Included are links to maizegdb and maizesequence.org genome views. The new data are also aligned with AcDs insertion sites for reverse genetics.
Three new genome databases are now live at PlantGDB:
RcGDB, a genome database for castor bean (Ricinus communis) based on the JGI draft genome;
MgGDB, a genome database for Monkeyflower (Mimulus guttatus) based on the JGI draft genome; and
MeGDB, a genome database for Cassava (Manihot esculentis) based on the JGI draft genome.
Data displayed include current gene annotations, splice-aligned cDNAs, EST and PUTs, and splice-aligned related species proteins. (11-15).
Brachopodium genome updated
The Brachypodium distachyon genome browser BdGDB has been updated to incorporate additional EST and cDNA alignments. Genome and annotations are unchanged.
AcDsTagging workshop announced
This is the first announcement for June 20-24, 2011 worshop for postdocs, graduate students and PIs who wish to use the maize transposon Ds in reverse genetics programs. This 5-day workshop will provide hands on training in genetic and molecular genetic techniques for Ds reverse genetics, in conjuction with online resources at PlantGDB.org. Location: Boyce Thompson Research Institute, Ithaca, NY, USA
More information is available on our Workshop Page. Online registration coming soon.(11-24)
Find Ds insertions close to my gene:
The AcDs insertion sites has mapped almost 2000 transposon Ds insertions throughout the maize genome, for reverse genetics. Enter a geneID below to display nearby Ds insertions and links to other tagging resources:
New Transcript Assemblies (10-28)
New and refreshed transcript assemblies (PUTs) based on GenBank Release 179 are now available from our EST Cluster page (Oct 28, 2010).
We are continuing to enhance and improve the Community Annotation tools at PlantGDB. We now provide Working Groups by invitation, allowing annotation teams to review, organize and even curate annotations within the group. Contact us if you would like to start a Working Group. Other enhancements include a "forgot password" service, a genome version filter for annotation lists, and a new Web tool for subscribing to the latest annotations via Atom. Community Annotation tools are available for all genome browsers at PlantGDB (October 15, 2010).
MtGDB (Medicago) genome browser updated (10-15)
The MtGDB genome database for barrel medic (Medicago truncatula) has been updated with the recent Mt3.0 genome assembly and gene annotations published by medicago.org. 9 pseudochromosomes and a concatenation of 148 unanchored BACS are displayed. The new assembly is splice-aligned with GenBank Release 179 transcript data from Medicago as well as Arabidopsis and Glycine max predicted proteins (October 15, 2010).
VvGDB (grape) genome browser updated (10-15)
The VvGDB genome database for wine grape (Vitis vinifera) has been updated with the recent 12X genome assembly and gene annotations published by Genoscope. 19 pseudochromosomes and 11 unmapped scaffolds are displayed. The new assembly is splice-aligned with GenBank Release 179 transcript data from grape as well as Arabidopsis and Medicago predicted proteins (October 15, 2010).
yrGATE tool new features(9-29)
On the Community Annotation Central page (ZmGDB example), click the "Subscribe to the latest yrGATE Annotations" link and follow the directions to create a newsfeed of the latest community annotations in your favorite newsreader (e.g. Google, myYahoo, etc.).
Forgot your password? No problem, we now have a "Forgot Password" option for registered annotators, available on any GDB login page.
For genomes with several assembly versions. you can now click "DB Version" number (0 is lowest) to view annotations only from that version (Sept. 29).
GenBank Release 179 is live(9-21)
GenBank Release 179.0 sequence data (close date 8-14-2010) are now live at PlantGDB, except for BLAST indices which are still being built. New PUT Assemblies are underway and will be ready in early October.
CpGAT reports exon origins (8-19)
The CpGAT* tool for automated, real-time gene structure annotation now reports the details of each exon origin (whether evidence ID, pasa assembly, or ab inito-derived) in the GFF3 output file. Access CpGAT from any PlantGDB genome browser. *Comprehensive plant Gene Annotation Tool, release 1.05
Community Annotation Features (8-5)
We have updated the yrGATE tool and the CommunityCentral database for commmunity annotation. Changes include a more consistent annotation naming scheme, and easier to navigate annotation tables. PLEASE NOTE that if you have previously annotated genes, the ID has been changed; the former ID is now part of the Description field and can be retrieved using Search. The Community Annotation system is available for all genome browsers at PlantGDB.
New AcDs Tagging Data (8-3)
AcDs Tagging insertion data for maize have been updated to include redundancy information, confirmation data and southern blot and ipcr images. See example of a Ds Insertion Line
CpGAT user-input sequence (7-26)
The CpGAT* tool for automated, real-time gene structure annotation now supports user-input sequences (genome region or RNA/protein datasets). Also, users can optionally choose "all monocots" or "all dicots" transcript datasets for analysis instead of by species. Access CpGAT from any PlantGDB genome browser. *Comprehensive plant Gene Annotation Tool
The yrGATE* tool for community annotation now allows users to specify annotation type and locus being annotated. Annotation IDs are auto-generated, with optional user-specified suffix. Access yrGATE from any PlantGDB genome browser; see PlantGDB Help for documentation and tutorials. *your Gene Annotation Tool for Eukaryotes
CpGAT tool updated (7-11)
The CpGAT* tool for automated, real-time gene structure annotation, now includes spliced-alignment evidence and homology information in the final GFF3 file. CpGAT structures are displayed in the genome browser and via yrGATE. Access CpGAT from any PlantGDB genome browser. Click to view CpGAT Schema. *Comprehensive plant Gene Annotation Tool
Placement of Ds transposons in maize genome (6-16)
The AcDs Project has implemented an improved method for placing Ds flanking sequences (fDs) in the maize genome, and the dataset has been extended to include the latest Ds- as well as Ac-flanking sequences. So far 1,936 independent insertions (barcodes) are placed with reasonable certainly in the maize RefGen_v1 assembly. The updated Browse Insertions page shows potential location(s)/quality for the putative insertions, as well as genes nearby the insertion site, and links to detailed information about the accession (see description). All insertions are displayed graphically in the ZmGDB genome browser, and the pictograms are now standardized to show the Ds insertion point at the 5' end of the insertion (see description).
Transcript Assembly Release (6-4)
>
New and refreshed transcript assemblies (PUTs) based on GenBank Release 177 are in progress and should be available within the next week (May 21, 2010).
New PUT assemblies include:
>GenBank Release 177.0 sequence data (freeze date April 16, 2010) are now available on our Download Page (May 21, 2010).
Maize gene models are quality-flagged (5-12)
Maize RefGen_v1 gene models at ZmGDB are now flagged for quality (i.e. coverage and potential alternative splicing) in a separate track. This flagged track is also displayed at MaizeGDB where users can click to amend/correct gene structure using PlantGDB's yrGATE tool. (May 12, 2010)
CpGAT annotation tool updated(5-12)
CpGAT (Comprehensive plant Gene Annotation Tool), a new PlantGDB tool for real-time gene structure annotation of any genomic region, now outputs multiple splice isoforms and computes UTR regions when evidence is available. Select a genome region in any genome browser and launch CpGAT by clicking "Predict Gene Structures". Output is a GFF3 file of gene structures. Coming soon: Online display of annotations. (May 12, 2010)
yrGATE community annotation tool updated (5-12)
The yrGATE tool for user gene annotation now includes Working Group and Gene Category options and a new Search feature. The Working Group category can be used by annotation teams or subteams wishing to track annotation progress. The Gene Category field can be used to define and track annotations by any desired category (gene class, pathway, location, etc.). Coming soon: Working Group user membership and ability to view annotations in progress in your group (May 12, 2010).
AcDs Seed Order Form is online (5-12)
The AcDs Tagging seed order form is now online! Researchers can submit an web request for maize seed containing Ds transposon insertions, mapped to the maize genome by estimated chromosome coordinate (see Browse Ds Insertions). (May 12, 2010)
AcDs Tagging Update (3-18)
The AcDs Tagging database at PlantGDB has been updated to display Ds transposon matches to the maize pseudochromosomes (RefGen_v1). Users can browse a list of "placed" insertions by chromosome coordinate (Browse Ds Insertions), search functional annotations with potential Ds insertions ((Protein Annotation Table), and order seed containing the mapped insertion (Seed Order Instructions). (March 15, 20010)
PlantGDB at Maize Genetics Conf., March 18-21 (3-12)
PlantGDB was represented at the 52nd Annual Maize Genetics Conference, March 18-21, 2010, Riva del Garda, Italy. Check out Poster 151, "Maize Community Annotation Project to Improve Gene Structures" in the 2010 meeting program. (March 12, 2010)
New Annotation Workflow at BioExtract (3-12)
The BioExtract Server has added a powerful new workflow for annotating genomic DNA, based on user-selected transcript and protein databases. The pipeline uses EVM (EVidence Modeler) to evaluate transcript- and ab initio-derived exons, and it outputs a GFF3-formatted file of optimal gene structures. A similar pipeline is available at PlantGDB for use with xGDB genome browsers (see next news item). (March 12, 2010)
New Annotation Tool at PlantGDB (3-12)
CpGAT (Comprehensive plant Gene Annotation Tool) allows users to annotate any genomic region using any combination of transcript and protein datasets. The pipeline uses EVM (EVidence Modeler) to evaluate transcript- and ab initio-derived exons, and it outputs a GFF3-formatted file of optimal gene structures. The pipeline is currently available in the maize genome browser ZmGDB (click "Annotation Pipeline") and will soon be available for all genomes. This pipeline is also available as a customizable workflow in the BioExtract Server (see previous news item). (March 12, 2010)
Community Annotation Tips (3-12)
The yrGATE tool for gene structure annotation sports new context-sensitive help icons: just click any help icon () for a popup explanation of each function or tool.(Example). (March 12, 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:
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)
2009 news
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).
BdGDB, a genome browser for the model grass species Brachypodium distachyon, is now available, based on the JGI v1.0 8x genome assembly. The assembly displayed comprises 271.15 Mb arranged in 5 pseudochromosomes. Display includes gene models, splice-aligned EST, cDNA, PUT assembly and Arabidopsis and rice predicated proteins (October 30, 2009).
Maize pseudochromosome browser
The pseudochromosome browser ZmGDB is now available, based on maizesequence.org Release 4a.53 and the golden path BAC assembly from AGI. Display includes gene models and yrGATE annotated genes; splice-aligned ESTs, cDNAs, NEW PUT assemblies, and sorghum and rice predicated proteins; Ds insertions; GSS assemblies; agp contigs; and masked regions. We continue to provide a separate, BAC-based ZmGDB (BAC) browser with the latest BAC data (October 16, 2009; PUTs added Nov 5).
GenBank Release 173
We have updated our sequence repository to GenBank Release 173.0, announced on August 26. We are now updating BLAST and GeneSeqer indices. (October 1, 2009).
New and Updated Transcript Assemblies (v.173)
New and refreshed transcript assemblies (PUTs) based on GenBank Release 173 are available for download and BLAST at PlantGDB.
New PUT assemblies include:
PlantGDB's genome browsers for Arabidopsis thaliniana (AtGDB), Medicago truncatula (MtGDB), and Oryza sativa (OsGDB) have been updated to the latest genome assembly and annotation version for each species. Splice-aligned transcript and related-species proteins from Version 171 are displayed as well as the latest transcript assemblies. In addition, the Lotus japonicus BAC-based genome browser (LjGDB) has been re-released, based on a pseudochromosome assembly available from kazuza.org (October 1, 2009).
CoGe Links
Genome Browsers at PlantGDB display spliced alignments to model species proteins, which are also listed in searchable Protein Alignment tables. These tables now provide hyperlinks to CoGe's GEvo (Genome Evolution) tool for exploring colinearity across multiple genomes. To try this, click "Protein Alignments" in the left menu of any Genome Browser, and then click a CoGe link icon in the genome-ordered list. For more details, see Genome Browser Help or ZmGDB Help (October 3, 2009).
Interface Improvements
Several features have been added to PlantGDB's genome browser interface, making it easier for users to configure tracks and display alternative data views. Genomic region, track order and view/hide configurations are now preserved within a session, and logged-in users can customize all configurations for later recall. You can give the new features a spin by visiting any PlantGDB Genome Browser home page (July 13, 2009).
CoGe alignments for maize
ZmGDB's Protein Alignment Table, displaying high quality spliced alignments of sorghum and rice gene models to maize BACs, now has direct hyperlinks to CoGe's GEvo (Genome Evolution) tool for multiple genome alignment. Click any table entry to generate real-time blastz or tblastx alignments to the matching regions of rice or sorghum at CoGe. - now loads all overlapping gene models in one GEvo window! (details) Similar links for other genomes at PlantGDBD are under development (updated July 30, 2009).
BAC/scaffold GmGDB
In addition to the pseudochromosome- based GmGDB (soybean) genome browser based on the JGI Glyma1 release, we have created an alternative GmGDB browser based on the previous scaffold-based Glyma0 assembly together with Glycine max BACS. This allows users to view legacy data as well as BAC sequences not included in the current assembly. View BAC/Scaffold GmGDB (July 13, 2009).
Primer analysis for AcDs
The new FindPrimers online tool allows rapid batchwise design of primers optimized for confirmation of Ds insertion in maize DNA (July 13, 2009)
External links
All external links at PlantGDB are now decorated with an icon indicating that the link navigates away from PlantGDB's pages. (July 30, 2009)
The AcDs Tagging project site for maize has been updated with new flanking sequences (fDs) and additional search and download features. Visit the Browse Insersions page for a current list of insertions placed to the maize genome, or use our fDs BLAST page to find out if your favorite maize gene has a Ds insertion. (May 22, 2009).
New feature: Add a genome track
PlantGDB's genome browsers can now display tracks served from a remote genome browser using our new DAS (Distributed Annotation Service) client. From any genome region, simply choose Configure -> Add Track from the track menu, and paste the DAS server URL. A list of DAS servers can be found on our DAS Overview page (May 5, 2009).
New feature: User control menu
PlantGDB's genome browsers have a new dropdown menu for tools and user settings. Track order can be customized with simple with drag and drop or click to hide. Check it out at ZmGDB (May 5, 2009).
Update to GenBank Release 171
We have updated our sequence repository to GenBank Release 171.0, which was announced on April 15. We are now updating BLAST and GeneSeqer indices. New and updated transcript assemblies will be available within approx. 1 month of the release (April 20, 2009).
Soybean genome browser updated
The GmGDB (soybean) genome browser has been updated to the latest assembly (20 pseudochromosomes) based on the JGI Glyma1 release. Glyma1 gene models are displayed along with splice-aligned soybean transcripts, PUT and microarray probes, and Arabidopsis and Medicago predicted proteins [April 8, 2009].
PlantGDB Website - Feedback
We appreciate all the feedback we've received since our design change in March. We are working hard to make additional improvements and bug fixes, and we continue to welcome your comments and suggestions! As always, our feedback form is the easiest way to contact us [April 7, 2009].
PlantGDB Website - Menus
The Search and Download menus have been consolidated under Sequence. To view all sequence data available at PlantGDB, go to Sequence -> Overview. The Help and About menus have been consolidated under Support. To view all support pages available at PlantGDB, go to Support -> About. [April 7, 2009].
Maize spliced alignments
ZmGDB, the genome browser for Zea mays has been udpated to has been updated to GenBank Release 169 EST/cDNA alignments. A new PUT Assembly for maize is in progress [March 11, 2009].
Maize gene models
ZmGDB now includes gene models from maizesequence.org's Version 3B.50 "Working Gene Set", displayed as a light-green track [March 11, 2009].
New DAS Server
PlantGDB's genome browsers now provide a DAS (Distributed Annotation Service) server for remotely viewing PlantGDB genome-aligned features (EST, PUT, and community annotation gene models) on a genome browser. Currently available for AtGDB and ZmGDB; see PlantGDB's DAS table for latest DAS resources and links [March 11, 2009].
AcDs Tagging Database
The AcDs Tagging pages at PlantGDB have been updated and expanded. New features include a searchable table of Ds insertions matching maize BACs, a new matching algorithm for BAC:fDs matches, and expanded support pages [March 11, 2009].
New Download Tool
Want to download all the splice-aligned ESTs, PUTs, or proteins from a genomic region? Try the new advanced search/download feature, available on all genome browsers at PlantGDB under the "Search by Region" link. You can also download gene models (transcript or protein) or a GenBank or GFF3-formatted version of the genomic region. HOT TIP: the GenBank-formatted output imports directly into Vector NTI [March 11, 2009].
New PlantGDB Design!
Starting March 11, 2009 Plantgdb.org features a new look and feel, improved navigation and support pages, and several new data features and tools (see below). We hope you enjoy exploring the new site, and encourage you to give us feedback if you encounter problems [March 11, 2009]
PlantGDB at Maize Genetics Conf.
PlantGDB was represented at the 51st Maize Genetics Conference (March 12-14, 2009) Poster #169 (What's New at PlantGDB for Maize?) [March 11, 2009].
Plant sequence from GenBank Release 169 (December 15, 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated. For more information, visit the Sequence Overview Page [Jan. 11, 2009].
Lotus japonicus genome update
LjGDB, the genome browser for Lotus japonicus, has been updated to incorporate the recently-published Lotus draft genome sequence (Sato et al., 2008) [January, 11 2009].
Soybean genome update
GmGDB, the genome browser for Glycine max, has been updated to Version 167a EST/cDNA and PUT assembly. [November, 2008].
2008 News
GenBank Release 167
Plant sequence from GenBank Release 167 (August 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated [Sept. 19, 2008].
PUTs release 167
Ten new and seven refreshed transcript assemblies (PUTs) based on GenBank Release 167 are available for download and BLAST at PlantGDB. See details at our cluster progress page (look for version 167a) [Sept. 19, 2008].
New publication: Sparks, M.E. & Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction.BMC Bioinformatics, 9, 381. [abstract] [provisional PDF] [Sept. 19, 2008]
GeneSeqer Tool Update
The online GeneSeqer spliced alignment tool at PlantGDB has been updated and expanded to include any plant species transcript dataset [Sept. 19, 2008].
Papaya genome browser
Genome browser for papaya (Carica papaya L.), is now available, based on the recently-published papaya genome sequence (Ming et al., 2008). The new CpGDB displays the 3,208 sequence scaffolds (obtained from GenBank) with spliced-alignment to papaya EST, cDNA, PUT, and predicted Arabidopsis proteins. [August 15, 2008]
Advanced Search tool
The Advanced Search feature for xGDB genome browsers has been expanded to include gene models (Gbk-mRNA) as well as additional sequence retrieval options. To access Search, select a genome browser from the 'Genomes' dropdown menu, and then click 'Search' in the xGDB header menubar. See an example at GmGDB. [August 15, 2008]
GAEVAL tables
GAEVAL tables display incongruities in gene models versus alignment evidence. GAEVAL tables are now accessible for all browsers from the right menubar under 'GAEVAL Problematic Gene Models'. See an example at GmGDB, or visit the GAEVAL Help page for further details [August 15, 2008].
New FAQ Page
Visit the new FAQ (Frequently Asked Questions) help page here. [August 15, 2008]
Plant sequence from GenBank Release 167 (August 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated [Sept. 19, 2008].
Ten new and seven refreshed transcript assemblies (PUTs) based on GenBank Release 167 are available for download and BLAST at PlantGDB. See details at our cluster progress page (look for version 167a) [Sept. 19, 2008].
New publication: Sparks, M.E. & Brendel, V. (2008) MetWAMer: eukaryotic translation initiation site prediction.BMC Bioinformatics, 9, 381. [abstract] [provisional PDF] [Sept. 19, 2008]
The online GeneSeqer spliced alignment tool at PlantGDB has been updated and expanded to include any plant species transcript dataset [Sept. 19, 2008].
Plant sequence from GenBank Release 165 (April 2008) has been uploaded to PlantGDB, and sequence download repository, ftp site and BLAST and GeneSeqer indices have been updated [June 3, 2008].
The ZmGDB genome browser for maize (Zea mays) has been updated to display spliced alignment to maize PUT assembly 163a, as well as to updated EST/cDNA datasets. A new track displays spliced alignment to sorghum predicted proteins from JGI. ZmGDB continues to provide daily annotation of maize BAC sequences deposited to GenBank by the Maize Genome Sequencing Consortium (www.maizesequence.org) [ June 3, 2008]
GAEVAL (Gene Annotation Evaluation) data summarizing incongruence between gene models and evidence alignments has been compiled for several genomes (Arabidopsis, rice, sorghum, soybean, Medicago, moss, poplar, maize). GAEVAL tables allow annotators to assess and prioritize the annotation needs for a genome. To access them, use the "GAEVAL Problematic Gene Models" link on each genome browser home page. See an example at GmGDB [June 3, 2008].
All-new PlantGDB Help Pages are now available at PlantGDB, including Genome Browsers, Community Annotation, FAQ, and a new Site Map. Please let us know how you like the new format and content [June 3, 2008]
A new Advanced Search feature is available for all xGDB genome browsers, featuring batch mode search and retrieval of upstream or downstream sequence data. Click the "Search" link from any genome browser home page, e.g. AtGDB [June 3, 2008]
The BioExtract Server workflow management tool (Menu>Tools>Collaborations>BioExtract) menus have been reconfigured to streamline query building [June 3, 2007].
Twenty-nine new transcript assemblies (PUTs) based on GenBank Release 165 are available for download and BLAST at PlantGDB. See details at our cluster progress page (look for version 165a) [June 3, 2008].
New transcript assemblies (PUTs) are available for maize (Zea mays) and rice (Oryza sativaJaponica and Indica groups), based on GenBank Release 163. New PUT assemblies are also available for four solanaceous species: Solanum chacoense, S. habrochaites, S. pennellii and Nicotiana sylvestris. See complete PUT list on the Assembly Progress Page. [April 17, 2008]
GmGDB, the BAC-based browser for soybean (Glycine max), has been updated to include genomic scaffolds from the recently released soybean draft genome. The 3,317 scaffolds of assembly release Glyma0 (JGI), as well as BACs from GenBank, have been splice-aligned to EST, cDNA, PUT, probe, and predicted proteins from both Arabidopsis and Medicago. Predicted gene set Glyma0.1b from JGI is also displayed [April 17, 2008].
PpGDB, a new genome browser for moss (Physcomitrella patens) is now available, based on the recently-published moss genome sequence ( Rensing et al., 2008). The 2,106 scaffolds of assembly release v.1.1 been splice-aligned to EST, cDNA, PUT, and predicted proteins from both Arabidopsis and rice. Predicted gene set Phypa1.1 from JGI is also displayed [April 17, 2008].
AtGDB, the chromosome-based browser for Arabidopsis thaliana, has been updated to display spliced aligments to A. thaliana PUT assembly version 163a as well as EST and cDNA sequence from GenBank Release 163 [April 17, 2008].
For the latest on genome-wide mutagenesis in maize using Ac/Ds transposons, visit the updated Ac/Ds Project Page [March 7, 2008].
PlantGDB has been updated to GenBank Release 163, and new parsed sequence datasets are now available for download and BLAST. [February 7, 2008].
The ASIP (Alternative Splicing in Plants) database now includes legumes Medicago truncatula and Lotus japonicus. See also: Wang, B.-B., O'Toole, M., Brendel, V., and Young, N. (2008) Cross-species alignments reveal novel and conserved alternate splicing events in legumes.BMC Plant Biology 8:17 doi:10.1186/1471-2229-8-17 [online article] [February 20, 2008].
PtGDB, the pseudochromosome-based browser for Populus trichocarpa, has been updated to include annotated gene models from JGI [February 7, 2008].
SbGDB, the new chromosome-based genome browser for Sorghum bicolor, has been updated to include Orya sativa predicted protein spliced alignments. Data and database download are also available [January 7, 2008].
PlantGDB now offers an ftp site for bulk download of plant sequence and transcript assemblies (PUTs), in addition to our web browser-based download portal. [February 7, 2008].
New publication: Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M.D., Lawrence, C.J., Lushbough, C. & Brendel, V. (2007) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Research, 2007, doi: 10.1093/nar/gkm1041. [ PubMed ID: 18063570 ] [ online article ] [January 7, 2008].
13 updated and 17 new transcript assemblies (PUTs) are available for download and BLAST at PlantGDB. See details at our cluster progress page. Notably, the Arabidopsis thaliana PUT assembly has been updated to v.163 and annotated with UniProt similarity.
VvGDB, a new chromosome-based genome browser for Vitis vinifera (wine grape), is now available, based on the recent release of the grape genome. VvGDB displays chromosome 1 - 19 alignments with V. vinifera EST, cDNA, transcript assemblies (PUT), microarray probe, and Arabidopsis predicted proteins as well as complete data and database download [November 7, 2007].
SbGDB, the genome browser for Sorghum bicolor has been updated to a chromosome-based browser following the release of the Sbi1 assembly for sorghum. SbGDB currently displays chromosome 1 - 10 alignments with sorghum EST, cDNA, GSS assembly, and transcript assemblies (PUT), with Oryza sativa predicted protein spliced alignments to come soon. Data and database download are also available [November 7, 2007].
The ZmGDB genome browser for Zea mays has a new home page and searchable BAC tables for Phase 1, 2, and 3 BACs, including chromosome number and BAC clone names [November 7, 2007].
The maize daily BAC annotation table now allows users to search for multiple BAC annotations at a time by pasting a list of BAC gi's [November 7, 2007].
The BioExtract Server workflow management tool now includes a feature for local data upload [November 7, 2007].
PlantGDB has been updated with GenBank Release 161 sequence data, and new PUT assemblies have been generated for 16 species: Allium cepa, Arachis hypogaea, Brassica napus, Brassica rapa, Centaurea maculosa, Cryptomeria japonica, Glycine max, Hordeum vulgare, Medicago truncatula, Nicotiana benthamiana, Nuphar advena, Ostreococcus lucimarinus, Picea sitchensis, Pseudotsuga menziesii, Raphanus raphanistrum, and Solanum lycopersicum. [September 15, 2007].
GmGDB, a BAC-based genome browser for Glycine max (soybean), has been updated with BAC alignments to EST, cDNA, transcript assemblies (PUT), probe, and Arabidopsis protein [September 15, 2007].
The BioExtract Server, a PlantGDB-hosted server for executing custom sequence analysis workflows, has been updated. New features include many more available Web services tools, options for adding local tools and local datasets, and a powerful new workflow management tool [September 15, 2007].
GhGDB, a new BAC-based genome browser for Gossypium hirsutum (cotton), is available with BAC alignments to EST, cDNA, transcript assemblies (PUT), probe, and Arabidopsis protein [August 15, 2007].
SlGDB, a BAC-based genome browser for Solanum lycopersicum (tomato; formerly Lycopersicum esculentum), has been updated with 314 additional BAC sequences and alignments to EST, cDNA, transcript assemblies (PUT), probe, and Arabidopsis. The LeGDB (Lycopersicum esculentum) genome browser has been deprecated [August 15, 2007].
The ZmGDB BAC annotation table for Zea mays, introduced in May, provides searchable, browsable rice protein annotations for all maize BACs. New annotation tables, with either rice or Arabidopsis protein annotations, are now available for all BAC-based genome browsers including HvGDB (Hordeum vulgare, barley), LjGDB (Lotus japonicus), SlGDB (Solanum lycopersicum, tomato), GmGDB (Glycine max, soybean), BrGDB (Brassica rapa, field mustard), TaGDB (Triticum aestivum, bread wheat), SbGDB (Sorghum bicolor, sorghum), and GhGDB (Gossypium hirsutum, cotton) [August 15, 2007].
The ZmGDB genome browser for Zea mays now links individual BACs to their equivalent at MaizeSequence.org [June 28, 2007]
The maize daily BAC annotation table has been updated with faster performance and new features, including multiple search modes and the ability to display BAC matches to Ds transposon tags. New help pages are also available. [June 18, 2007]
The MtGDB genome browser for Medicago truncatula has been updated to display pseudochromosomes aligned to PUT, probes, EST/cDNA, and Arabidopsis predicted protein alignments. [June 1, 2007].
The AtGDB genome browser for Arabidopsis thaliana has been updated to TAIR7. [June 1, 2007]
The ZmGDB genome browser for Zea mays now includes a daily update of new maize BAC sequences deposited in GenBank by the maize genome project. Alignments to PUT, GSS, EST/cDNA, rice predicted proteins, microarray probes, and fDs are displayed for each BAC. A new annotation table is available for browsing the latest BACs and annotated proteins from rice. Up-to-date maize BAC sequences are also available for download and BLAST. [May 16, 2007].
The OsGDB genome browser for Oryza sativa has been updated to TIGR genome build 5.0. A new track is available showing Arabidopsis thaliana predicted protein alignments. [May 16, 2007].
The PtGDB genome browser for Populus trichocarpa has been updated to display pseudochromosomes aligned to PUT, EST/cDNA, and Arabidopsis predicted protein alignments. [May 16, 2007].
Several new analysis tools have been added: Tracembler, which allows the user to do chromosome walks with pre-assembly trace data; MuSeq Box, a tool for generating tabular output from multiple BLAST queries; and TE Nest, for annotation and visualization of nested transposable elements in maize. [May 16, 2007]
We recently migrated PlantGDB.org to a new server for improved performance. Please let us know if you experience any problems using the site. Thank you! [May 16, 2007]
[Apr. 2006]
AtGDB has been updated with PlantGDB 152a version of Arabidopsis ESTs, cDNAs, and PUTs. The number of ESTs increased about 50% from 151a version.
[Feb. 2006]
AtGDB has been updated to incorporate the TAIR version 6.0 genome release, PlantGDB 151a version of Arabidopsis ESTs, cDNAs, PUTs, and Affymetrix microarray probes.
[Feb. 2006]
OsGDB has been updated to incorporate the TIGR Version 4 genome assembly and annotation as well as the PlantGDB 151a version of rice PUTs and Affymetrix microarray probes.
[Feb. 2006]
ZmGDB is up to date with respect to the PlantGDB 151a version of maize BACs, ESTs, cDNAs, PUTs, and GSS contigs. The browser now also links Maize Oligonucleotide Array Project probes.
[Feb.2006]
The Affymetrix Arabidopsis, soybean, tomato, Medicago, rice, sugar cane, wheat, and grape, maize and the Maize Oligonucleotide Array Project probes have been mapped to PUT version 151a contigs and linked to the PLEXdb expression database (see an example). You can search for matches against these probe sequences using our ProbeMatch tool.
[Jul. 2005] The Plant Genomics Community can access our
alignment data through DAS
[Jul. 2005] Annotation for
Amateurs: a complete teaching module that teachers
can adopt for classroom use and which is also
appropriate for anyone new to gene annotation. All are
invited to become a member of the growing Annotation
Community!
) for a popup explanation of each function or tool.(Example). (March 12, 2010)