Database Commons
Database Commons

a catalog of worldwide biological databases

Database Profile

PlantGDB

General information

URL: http://www.plantgdb.org/
Full name:
Description: PlantGDB is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services.
Year founded: 2005
Last update: 2015-07-01
Version: v1.0
Accessibility:
Manual:
Unaccessible
Country/Region: United States

Classification & Tag

Data type:
DNA
Data object:
Database category:
Major species:
NA
Keywords:

Contact information

University/Institution: Iowa State University
Address: Ames IA 50011, USA
City: Ames
Province/State: Iowa
Country/Region: United States
Contact name (PI/Team): Volker Brendel
Contact email (PI/Helpdesk): vbrendel@iastate.edu

Publications

18063570
PlantGDB: a resource for comparative plant genomics. [PMID: 18063570]
Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V.

PlantGDB (http://www.plantgdb.org/) is a genomics database encompassing sequence data for green plants (Viridiplantae). PlantGDB provides annotated transcript assemblies for >100 plant species, with transcripts mapped to their cognate genomic context where available, integrated with a variety of sequence analysis tools and web services. For 14 plant species with emerging or complete genome sequence, PlantGDB's genome browsers (xGDB) serve as a graphical interface for viewing, evaluating and annotating transcript and protein alignments to chromosome or bacterial artificial chromosome (BAC)-based genome assemblies. Annotation is facilitated by the integrated yrGATE module for community curation of gene models. Novel web services at PlantGDB include Tracembler, an iterative alignment tool that generates contigs from GenBank trace file data and BioExtract Server, a web-based server for executing custom sequence analysis workflows. PlantGDB also hosts a plant genomics research outreach portal (PGROP) that facilitates access to a large number of resources for research and training.

Nucleic Acids Res. 2008:36(Database issue) | 139 Citations (from Europe PMC, 2024-12-21)
16219921
Comparative plant genomics resources at PlantGDB. [PMID: 16219921]
Dong Q, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V.

PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models (for Arabidopsis, see the AtGDB site at http://www.plantgdb.org/AtGDB/; for rice, see the OsGDB site at http://www.plantgdb.org/OsGDB/). In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database.

Plant Physiol. 2005:139(2) | 49 Citations (from Europe PMC, 2024-12-21)

Ranking

All databases:
1059/6266 (83.115%)
Gene genome and annotation:
342/1780 (80.843%)
Expression:
195/1210 (83.967%)
1059
Total Rank
188
Citations
9.895
z-index

Community reviews

Not Rated
Data quality & quantity:
Content organization & presentation
System accessibility & reliability:

Word cloud

Related Databases

Citing
Cited by

Record metadata

Created on: 2015-07-27
Curated by:
Lina Ma [2018-06-11]
Dong Zou [2018-02-13]
Shixiang Sun [2016-03-25]
Shixiang Sun [2015-11-21]
Zhang Zhang [2015-10-20]