Plant DNA Designing Web Application: PromoterCAD

June 21, 2013

The RIKEN Center for Sustainable Resource Science and the RIKEN Advanced Center for Computing and Communication (ACCC) have jointly developed a web application called “PromoterCAD” for designing synthetic DNA promoter sequences that control gene expression in plants. PromoterCAD utilizes existing life science databases such as microarray expression data.

PromoterCAD has an easy-to-use interface that allows users without specialized computer programming knowledge to design synthetic promoters to control where (in what organs) and when gene expression takes place in the model plant Arabidopsis. Users can also freely add data or customize PromoterCAD.

The developers are aiming to make PromoterCAD into a more versatile program for synthetic promoter design by furthering the integration of databases and expanding applicability beyond plants to the design of animal DNA. Such versatility could lead to possible applications for synthetic biology not only in the environmental field but also in medicine.

Original article
Nucleic Acids Research doi:10.1093/nar/gkt518
R. S. Cox III, K. Nishikata, S. Shimoyama, Y. Yoshida, M. Matsui, Y. Makita, T. Toyoda,
"PromoterCAD: data-driven design of plant regulatory DNA".
Minami Matsui
Team Leader
Synthetic Genomics Research Team, Biomass Engineering Program Cooperation Division