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GABI-Kat SimpleSearch database


NAR Molecular Biology Database Collection entry number 935
Weisshaar, Bernd; Kleinboelting, Nils; Huep, Gunnar; Kloetgen, Andreas; Viehoever, Prisca
1Institute of Genome Research, Center for Biotechnology (CeBiTec), Bielefeld University, Universitaetsstrasse 25, D-33594 Bielefeld, Germany
2 Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Koeln, Germany

Database Description

Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently the database contains more than 108,000 mapped FSTs from about 64,000 lines which cover 64 percent of all annotated A. thaliana protein-coding genes. The web interface allows to search for relevant insertions by gene code, keyword, line identifier, GenBank accession number of the FST, and also by BLAST. A graphic display of the genome region around the gene or the FST location assists users to select insertion lines of their interests. About 3,800 insertions were confirmed in the offspring of the plant from which the original FST was generated, and the seeds of these lines are available from the Nottingham Arabidopsis Stock Centre. The database now also contains additional information such as segregation data, gene-specific primers and confirmation sequences. This information not only helps users to evaluate the usefulness of the mutant lines, but also covers a big part of the molecular characterization of the insertion alleles.

Acknowledgements

GABI-Kat was supported by the Federal Ministry of Education and Research (BMBF) in the context of the German plant genomics program GABI (grant no. 0312273).

References

1. Li, Y., Rosso, M.G., Strizhov, N., Viehoever, P. and Weisshaar, B. (2003) GABI-Kat SimpleSearch: a flanking sequence tag (FST) database for the identification of T-DNA insertion mutants in Arabidopsis thaliana. Bioinformatics, 19, 1441-1442.

Category: Plant databases
Subcategory: Arabidopsis thaliana

Go to the abstract in the NAR 2012 Database Issue.
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