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Results
1, Theoretical model of predicting efficiency of terminators
The goal of theoretical model to predict the efficiency of a terminator from its
nucleotide sequence. We use free energy methods to predict the secondary structure
of terminator. A d score is defined as
D=-96.6DΔ/L+18.6T-116.9 (2)
Here, ΔG is the Gibbs free energy change of stemloop formation. L is the length of stemloop. T is the score of T tail.
To get a relationship between d score and efficiency, we use the biofab data as training dataset. Biofab is the International Open Facility Advancing Biotechnology, which was founded in 2009. It's led by bioengineers from UC Berkeley and Stanford. In biofab data, there are 40 terminators with efficiency data available. We calculated the d score of terminators in Biofab and plot it with efficiency (Figure 1).
(Figure 1 diagram showing the correlation between d score and efficiency)
We found that d score and efficiency is positively correlated. Linear fitting is
performed and the fitting curve is
E=1.4D+39.1 (2)
The R^2 is 0.54.
We proposed that terminators can be classified into three classes based on efficiency.
(Table.1 Table of efficiency and d score correspond to different class of terminators).
2, Validating theoretical model by existing data
We collect existing data of efficiency of terminators from literatures and databases except Biofab. Using these data, we plot the predicted efficiency based on formula (2) with efficiency data (Figure 2). We found that our theoretical predication fit experiemental data quite well with correlation coefficient 0.8
(Figure 2, diagram of validation using our experimental data)
3, TTEC software and webtool
We developed TTEC software to predict terminator efficiency, which is available at
www.terminator efficiency.com (for our web tool)
https://github.com/igemsoftware/SUSTC_Shenzhen_B_2012 (for our software)
(Figure 3 the interface of our web tool)
(Figure 4 the intrface of outr software)
4, Database of terminator efficiency
We built a database of terminators whose efficiency had been measured. Not only terminator efficiency , other information such as the direction, category and structure are also included. Some of the data were from partsregistry and Biofab.Terminator Library. Others were from papers. We read many papers to find those terminators and some of the information were got through our e-mail with the author.The database will continue to update to give it more utility.
（Figure 5 our database of terminators whose efficiency have been measured）
