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Nucleic Acids Research Advance Access published online on October 24, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl753
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Paper

GABI-Kat SimpleSearch: an Arabidopsis thaliana T-DNA mutant database with detailed information for confirmed insertions

Yong Li1,2, Mario G. Rosso1,2, Prisca Viehoever1 and Bernd Weisshaar1,*

1 Institute 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

*To whom correspondence should be addressed. Tel: +49 521 106 6873; Fax: +49 521 106 6423; Email: bernd.weisshaar{at}uni-bielefeld.de

Received August 15, 2006. Revised September 25, 2006. Accepted September 25, 2006.

Insertional mutagenesis approaches, especially by T-DNA, play important roles in gene function studies of the model plant Arabidopsis thaliana. GABI-Kat SimpleSearch (http://www.GABI-Kat.de) is a Flanking Sequence Tag (FST)-based database for T-DNA insertion mutants generated by the GABI-Kat project. Currently, the database contains >108 000 mapped FSTs from ~64 000 lines which cover 64% of all annotated A.thaliana protein-coding genes. The web interface allows searching 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 assists users to select insertion lines of their interests. About 3500 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.


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[Abstract] [Full Text] [PDF]


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