Our project incorporated the use of Software such as 'UTR' Designer (Seo et al. 2013) . Additionally, we utilized the computational tool of the COBRA (Constraint-based Reconstruction and Analysis) Toolbox for the MATLAB platform.
'UTR' Designer is a software meant to "predict prokaryotic translation efficiency which can applied for optimizing bacterial hosts for the production of biochemical compounds or recombinant proteins" (Seo et al. 2013). The software can either predict the expression level from a known input sequence, or it can help you design appropriate 5' UTR sequences for certain desired expression levels. We utilized this predictive software to see if it were applicable to Methanococcus maripaludis by allowing it to predict the expression level from our known mutation sequences and comparing their theoretical results with our experimental results. Our results can be seen on our Modeling page.
The Cobra Toolbox utilizes the MATLAB platform so that people can perform “Constraint-based Reconstruction and Analysis.” Our team took advantage of this toolbox to perform flux balance analysis on our organism Methanococcus maripaludis.
Seo, Sang W. et al. Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. (2013) Metabolic Engineering. Vol. 15 pg. 67-74.