Arabidopsis Bioinformatics

Written by Super User. Posted in Botany

Learn about Arabidopsis bioinformatics.

At Molecular Station Arabidopsis Thaliana Bioinformatics, you will find all the botany and arabidopsis bioinformatics tools and databases.

Also see our online compendium of Bioinformatics on Arabidopsis Thaliana and Databases

 

Do you need an Arabidopsis Thaliana Knock-out?

With the availability of the arabidopsis genomic sequence, the functions of all the predicted genes will need to be uncovered. Currently, the functions about more than 25,000 genes in this botany reference plant are unknown.

An cost-effective and efficient method to identify the functions of these genes is through insertional mutagenesis screens. These screens have been accomplished using insertional mutagenesis using the Agrobacterium which inserts T-DNA into the Arabidopsis genome.

The Salk Institute Genome Analysis Laboratory (SIGnAL) is currently using high-throughput genome sequencing methods and has identified many of the sites of insertion of Agrobacterium T-DNA into the Arabidopsis genome. Transformed T-DNA inserted plants from the Alonso/Crosby/Ecker arabidopsis collection are grown and genomic DNA is recovered from these plants.  T-DNA insertions with flanking DNA arabidopsis sequence is recovered and then sequenced. Alignment of these insertional arabidopsis genomic sequences with the whole arabidopsis genome allow the determination of which arabidopsis plant seeds contain insertional mutations and where. This information is entered into a database, annotated by gene and sequence, which then allows researchers to determine which gene or sequence has been knocked-out. One can then order seeds which contain the knock-out or insertional-mutation of interest. The data is now available via a web accessible graphical interface, and one can search by text string or sequence.

To search:

SIGnAL "T-DNA Express" Arabidopsis Gene Mapping Tool

 

Arabidopsis DNA sequences are available at:

GenBank and

(TAIR) The Arabidopsis Information Resource

 

To Obtain Arabidopsis Seeds with Insertional-mutations or Knock-outs:

ABRC Arabidopsis Biological Resource Center

 

Also see:

T-DNA Express (SIGnAL Arabidopsis Gene Mapping Tool). Alternatively you may download all data used in the T-DNA Express

Download all T-DNA genome integration site sequences

Of interest:

Arabidopsis 2010: Tools and Technologies to Enable Genome-Wide Screens in Arabidopsis

See Protocols on Arabidopsis

See our online compendium of Bioinformatics on Arabidopsis Thaliana and Databases display_block('arabidopsis'); ?>