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PlantGDB


NAR Molecular Biology Database Collection entry number 355
Dong, Q.1, Schlueter, S.D.1, Brendel, V.1,2
1Department of Genetics, Development and Cell Biology and 2Department of Statistics, Iowa State University, Ames, IA 50011-3260, USA

Database Description

PlantGDB is a database of plant genomic sequences, in particular Expressed Sequence Tags (ESTs) that correspond to fragments of genes that are actively transcribed under particular conditions. For each of 48 species, 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 will provide snapshots of the current knowledge of plant gene composition and facilitate our understanding of plant genetics and evolution. AtGDB (http://www.plantgdb.org/AtGDB; Arabidopsis thaliana GDB) is our model species-specific plant GDB in the case that the entire genome of the species is available. Each EST has been mapped to its putative cognate location in the genome. Visual and textual displays show all the spliced alignments, together with current genome gene structure annotation and full-length cDNA evidence. Linked sequence similarity search and spliced alignment tools provide a convenient interface to view, verify, and correct gene structure annotation.

Acknowledgements

PlantGDB is supported by the U.S.A. National Science Foundation Plant Genome Research grant DBI-0321600.

References

1. Dong,Q., Schlueter,S.D., Brendel,V. (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Research 32,

Category: Plant databases

Go to the abstract in the NAR 2008 Database Issue.
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