Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/31/2007
Publication Date: 12/6/2007
Citation: 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. 36:D959-965. Interpretive Summary: PlantGDB is a database of plant sequences that has tools and services that enable researchers to utilize sequence information more efficiently. Because information from other species is useful for understanding the genome of a species of interest, comparative functionalities are included as one example of the views PlantGDB serves. Methods of visualizing sequence data are made available in addition to services to download data directly for off-site use. For plant breeders, such sequence-based capabilities help to speed the process of creating molecular markers for crop improvement.
Technical 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 13 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.