Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2005
Publication Date: 10/3/2005
Citation: Dong, Q., Lawrence, C.J., Schlueter, S.D., Wilkerson, M.D., Kurtz, S., Lushbough, C., Brendel, V. 2005. Comparative plant genomics resources at PlantGDB. Plant Physiology. 139(2):610-618. Interpretive Summary: PlantGDB (Plant Genetic Data Base) is a project that seeks to develop plant species-specific molecular sequence databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities. This paper informs the readership of “Plant Physiology” of the breadth of information made available through PlantGDB; explains where the information comes from and how it is analyzed, curated, and made accessible; describes analysis tools made available at the Website; and reveals how the database infrastructure was built and is presently maintained.
Technical Abstract: PlantGDB (http://www.plantgdb.org) is a database of plant molecular sequences. 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. GSS sequences are assembled similarly. The resulting GSS contigs are matched to ESTs and conserved protein homologs to identify putative full-length ORF-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis and rice, 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.