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Nucleic Acids Research Advance Access originally published online on December 6, 2007
Nucleic Acids Research 2008 36(Database issue):D959-D965; doi:10.1093/nar/gkm1041
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Nucleic Acids Research, 2008, Vol. 36, Database issue D959-D965
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article appears in the following Nucleic Acids Research issue: Database issue [View the issue table of contents]

Articles

PlantGDB: a resource for comparative plant genomics

Jon Duvick1, Ann Fu1, Usha Muppirala1, Mukul Sabharwal1, Matthew D. Wilkerson1, Carolyn J. Lawrence2, Carol Lushbough3 and Volker Brendel4,5,*

1Department of Genetics, Development and Cell Biology, Iowa State University, 2USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, 3Department of Computer Science, University of South Dakota, Vermillion, SD 57069, 4Department of Genetics, Development and Cell Biology and 5Department of Statistics, Iowa State University, Ames IA 50011, USA

*To whom correspondence should be addressed. Tel: +1 515-294-9884; Fax: +1 515-294-6755; Email: vbrendel{at}iastate.edu

Received September 12, 2007. Revised October 30, 2007. Accepted October 31, 2007.

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.


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