Campus Units
Genetics, Development and Cell Biology, Statistics, Bioinformatics and Computational Biology
Document Type
Article
Publication Version
Published Version
Publication Date
2008
Journal or Book Title
Nucleic Acids Research
Volume
36
Issue
suppl 1
First Page
D959
Last Page
D965
DOI
10.1093/nar/gkm1041
Abstract
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.
Rights
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.
Copyright Owner
The Authors
Copyright Date
2007
Language
en
File Format
application/pdf
Recommended Citation
Duvick, Jon; Fu, Ann; Muppirala, Usha; Sabharwal, Mukul; Wilkerson, Matthew D.; Lawrence, Carolyn J.; Lushbough, Carol; and Brendel, Volker, "PlantGDB: a resource for comparative plant genomics" (2008). Genetics, Development and Cell Biology Publications. 48.
https://lib.dr.iastate.edu/gdcb_las_pubs/48
Comments
This article is from Nucl. Acids Res. (2008) 36(suppl 1): D959–D965.doi: 10.1093/nar/gkm1041. Posted with permission.