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Plant Physiology 139:610-618 (2005)
© 2005 American Society of Plant Biologists

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Bioinformatics

Comparative Plant Genomics Resources at PlantGDB1

Qunfeng Dong, Carolyn J. Lawrence2, Shannon D. Schlueter, Matthew D. Wilkerson, Stefan Kurtz, Carol Lushbough and Volker Brendel*

Department of Genetics, Development and Cell Biology (Q.D., C.J.L., S.D.S., M.D.W., V.B.), and Department of Statistics (V.B.), Iowa State University, Ames, Iowa 50011–3260; Zentrum für Bioinformatik, Universität Hamburg, 20146 Hamburg, Germany (S.K.); and Department of Computer Science, University of South Dakota, Vermillion, South Dakota 57069 (C.L.)

PlantGDB (http://www.plantgdb.org/) is a database of plant molecular sequences. Expressed sequence tag (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. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), 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.

1 This work was supported by the National Science Foundation Plant Genome Research Projects (grant no. DBI–0321600 to V.B. and C.L.).

2 Present address: Corn Insects and Crop Genetics Research, U.S. Department of Agriculture Agricultural Research Service and Department of Agronomy, Iowa State University, Ames, IA 50011–3260.

www.plantphysiol.org/cgi/doi/10.1104/pp.104.059212.

* Corresponding author; e-mail vbrendel{at}iastate.edu; fax 515–294–6755.

Received December 31, 2004; returned for revision May 4, 2005; accepted May 12, 2005.




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