ATIDB: Arabidopsis thaliana insertion database.

Xiaokang Pan; Hong Liu; Jonathan Clarke; Jonathan Jones; Mike Bevan; Lincoln Stein

doi:10.1093/nar/gkg222

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ATIDB: Arabidopsis thaliana insertion database.

Xiaokang Pan·Hong Liu·Jonathan Clarke·Jonathan Jones·Mike Bevan·Lincoln Stein

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Abstract

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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Amino Acid Sequence Arabidopsis Binding Sites Databases, Factual Genome, Plant Internet Molecular Sequence Data Mutagenesis, Insertional Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

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Xiaokang Pan, Hong Liu, Jonathan Clarke, Jonathan Jones, Mike Bevan, Lincoln Stein. 2003-02-15. ATIDB: Arabidopsis thaliana insertion database.. https://doi.org/10.1093/nar%2Fgkg222

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