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Nucleic Acids Res. 2008 Jan;36(Database issue):D959-65. Epub 2007 Dec 6.

PlantGDB: a resource for comparative plant genomics.

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  • 1Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.

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.

PMID:
18063570
[PubMed - indexed for MEDLINE]
PMCID:
PMC2238959
Free PMC Article

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