Arabidopsis Motif Scanner

Arabidopsis Motif Scanner is a specialized application created to help researchers analyze gene relations and functions.

It enables you to pinpoint the position of cis-regulatory elements in the “Arabidopsis thaliana” plant commonly used as a model organism in biology and genetics, as well as combine this information with other data to identify gene networks regulated by transcription factors.

Arabidopsis Motif Scanner, as its name suggests, allows you to analyze the genome of the “Arabidopsis thaliana” plant, and it provides you with a comprehensive database that includes annotations and gene interactions for each result.

Moreover, it makes it possible to combine the extracted information with NGS and DNA Chip Array results in order to discover new gene relations and functions.

Arabidopsis Motif Scanner uses DNA-protein and protein-protein interaction data to help you identify metabolic pathways regulated by specific transcription factors.

Upon launch, the application loads the database and displays the Motif Scanner tab. Here, you can perform searches based on a number of parameters, as well as filter the results.

The Expression tab enables you to combine cis-acting element positions with NFS or DNA Chip Array expression data. You can change the Fold Change Threshold, filter the results and export all the entries or just the selected ones.

You can view the gene organization in the Gene Viewer tab either by clicking on the AGI code box in the Motif Scanner tab or by inserting the code in the specified field.

Lastly, after clicking and of the EC or Interactions cells in the Motif Scanner tab, you can view the resulting data in a tree view within the Interactions tab.

Even though the application is clearly targeted at experienced researchers, it is worth noting that a comprehensive user manual is available online. Because of this, it should not take very long for first-time users to get the hang of things and start taking advantage of this helpful research tool.

In conclusion, Arabidopsis Motif Scanner is a powerful software solution that allows you to correlate cis-acting element position information with NGS or DNA Chip Array expression data, making it possible to discover new gene relations and functions.