ATIDB: Arabidopsis thaliana insertion database

Pan, X. K., Liu, H., Clarke, J., Jones, J., Bevan, M., Stein, L. (February 2003) ATIDB: Arabidopsis thaliana insertion database. Nucleic Acids Research, 31 (4). pp. 1245-1251. ISSN 0305-1048

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URL: http://www.ncbi.nlm.nih.gov/pubmed/12582244
DOI: 10.1093/nar/gkg222

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.

Item Type: Paper
Uncontrolled Keywords: DROSOPHILA GENOME PROJECT FUNCTIONAL GENOMICS T-DNA PLANT DEVELOPMENT MUTAGENESIS EXPRESSION TRAP
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
CSHL Authors:
Communities: CSHL labs > Stein lab
Depositing User: Matt Covey
Date: February 2003
Date Deposited: 01 Jul 2013 20:29
Last Modified: 01 Jul 2013 20:29
PMCID: PMC150240
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27885

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