Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Bioinformatics: Databases
           Computer: Poster and Demo

PlantGDB - PLANT GENOME DATABASE AND ANALYSIS TOOLS

¹ Department of Zoology and Genetics, Iowa State University, Ames, IA 50011-3260, U.S.A.

² Department of Zoology and Genetics and Department of Statistics, Iowa State University, Ames, IA 50011-3260, U.S.A.

PlantGDB (www.plantgdb.org) is a database of all major plants genomic sequences, in particular Expressed Sequence Tags (ESTs) that correspond to fragments of genes that are actively transcribed under particular conditions. The database organizes the ESTs into contigs that represent tentative unique genes. The contigs are annotated and, whenever possible, linked to their genomic DNA origins. The PlantGDB web site includes a number of bioinformatics tools that facilitate gene prediction and cross-species comparisons. The database provides snapshots of the current knowledge of plant gene composition and facilitates our understanding of plant genetics and evolution. It also provides basis for identifying sets of genes common to all plants or specific particular species. In the first year of this project, we have concentrated on setting up the BLAST (www.zmdb.iastate.edu/cgi-bin/PlantGDBblast) and GeneSeqer (bioinformatics.iastate.edu/cgi-bin/gs.cgi) web services that allow users to find ESTs of interest across all species (using BLAST) and thread ESTs into genomic DNA (using GeneSeqer). The latter will produce gene structure models based on EST evidence. Another major focus of our efforts has been to provide complete analysis of EST and cDNA evidence for gene models in Arabidopsis. This has resulted in the AtGDB site (www.plantgdb.org/AtGDB.html) where all the evidence is conveniently viewable and linked to further analysis tools. In addition, web-based curation system is provided for the research community annotation. In the next step, we will extend our working models and technologies used in the AtGDB and separately funded ZmDB (www.zmdb.iastate.edu) to all other plants, with or without whole genome sequences.