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Nucleic Acids Research, 2003, Vol. 31, No. 4 1245-1251
© 2003 Oxford University Press

ATIDB: Arabidopsis thaliana insertion database

Xiaokang Pan, Hong Liu1, Jonathan Clarke2, Jonathan Jones3, Mike Bevan2 and Lincoln Stein*

Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, 1 Aventis Pharmaceuticals Inc., Bridgewater, NJ 08807, USA, 2 The John Innes Centre, Colney Lane, Norwich NR4 7UH, UK and 3 Sainsbury Laboratory, The John Innes Centre, Norwich NR4 7UH, UK

*To whom correspondence should be addressed. Tel: +1 516 367 8380; Fax: +1 516 367 8389; Email: lstein{at}cshl.edu

Insertional mutagenesis techniques, including transposon- and T-DNA-mediated mutagenesis, are key resources for systematic identification of gene function in the model plant species Arabidopsis thaliana. We have developed a database (http://atidb.cshl.org/) for archiving, searching and analyzing insertional mutagenesis lines. Flanking sequences from approximately 10 500 insertion lines (including transposon and T-DNA insertions) from several tagging programs in Arabidopsis were mapped to the genome sequence through our annotation system before being entered into the database. The database front end provides World Wide Web searching and analyzing interfaces for genome researchers and other biologists. Users can search the database to identify insertions in a particular gene or perform genome-wide analysis to study the distribution and preference of insertions. Tools integrated with the database include a graphical genome browser, a protein search function, a graphical representation of the insertion distribution and a Blast search function. The database is based on open source components and is available under an open source license.


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