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ATIDB: Arabidopsis thaliana insertion database.

Xiaokang Pan1, Hong Liu, Jonathan Clarke

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.

Nucleic Acids Research
|February 13, 2003
PubMed
Summary
This summary is machine-generated.

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Researchers created a database for Arabidopsis thaliana insertional mutagenesis lines, aiding gene function discovery. This resource enables genome-wide analysis of transposon and T-DNA insertions for plant biology research.

Area of Science:

  • Plant genetics and genomics
  • Bioinformatics and computational biology

Background:

  • Insertional mutagenesis, using transposons and T-DNA, is crucial for identifying gene function in Arabidopsis thaliana.
  • Systematic analysis of large-scale insertion mutant collections is essential for comprehensive functional genomics.

Purpose of the Study:

  • To develop a centralized, searchable database for archiving and analyzing insertional mutagenesis lines in Arabidopsis thaliana.
  • To provide researchers with tools for identifying specific insertion sites and analyzing insertion patterns across the genome.

Main Methods:

  • Mapping flanking sequences from ~10,500 transposon and T-DNA insertion lines to the Arabidopsis thaliana genome.
  • Developing a web-based database (http://atidb.cshl.org/) with search and analysis functionalities.

Related Experiment Videos

  • Integrating tools such as a genome browser, protein search, insertion distribution visualization, and BLAST search.

    • Main Results:

    • Successfully mapped and integrated data from over 10,500 insertion lines into the database.
    • Provided user-friendly web interfaces for searching individual genes and performing genome-wide insertion distribution analyses.
    • The database is built on open-source components, ensuring accessibility and adaptability.

    Conclusions:

    • The developed database serves as a valuable resource for the Arabidopsis research community.
    • Facilitates efficient exploration of gene function through systematic analysis of insertional mutagenesis data.
    • Promotes further functional genomics studies in Arabidopsis thaliana.