Team:SUSTC-Shenzhen-B/achievements

From 2012.igem.org

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<h1><p>Achievements</p></h1>
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<h1><p>Results</p></h1>
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                 <h3 class="STYLE13">1. Function of our Web Tool and PC Software</h3>
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                 <h3>1, Theoretical model of predicting efficiency of terminators</h3>
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<p>When a terminator sequence was entered, our software would output the secondary structure of the terminator based on Energy Minimization Rule and the termination efficiency.</p>
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<p>Besides, we made a database which includes many efficiency-measured terminators and some basic information of them.</p>
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<img src="http://2012.igem.org/wiki/images/8/8a/%E6%97%A0%E6%A0%87%E9%A2%98.png" class="img_fl img_border" />
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<h3 class="STYLE13">2. Calculation of Terminator Efficiency</h3>
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<p>We calculate the D score of several terminators we got from Biofab. Terminator Library. Then we made a simulation formula of D score and termination efficiency based on the efficiency data in that terminator library and the score we calculated. We made a linear fitting and the R^2 is 0.54. The picture below shows the results:</p><p>
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<img src="http://2012.igem.org/wiki/images/a/a1/%E6%97%A0%E6%A0%87%E9%A2%981.png" class="img_fl img_border" /></p>
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<br>
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<p>(Figure 1:The x-axis is d score and the y-axis is termination  efficiency)</p>
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<p>Our lab group did experiments to measure efficiency of some terminators. We chose five of them to see if the prediction of TTEC(the software we created to predict terminator efficiency) works well. The picture below shows the results. The x-axis is the efficiency data we got from our experiments and the y-axis is the efficiency predicted by TTEC. We can see that the slope of linear fitting is closed to 1 and the R^2 is 0.621.</p>
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<p>
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<img src="http://2012.igem.org/wiki/images/3/33/%E6%97%A0%E6%A0%87%E9%A2%982.png" class="img_fl img_border" /></p>
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<p>(Figure 2)</p>
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<p>We thought the results were good but we would continue to improve our prediction in future.</p>
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<h3 class="STYLE13">3. Our Database</h3>
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<p>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.</p>
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<p>The goal of theoretical model to predict the efficiency of a terminator from its
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nucleotide sequence. We use free energy methods to predict the secondary structure
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of terminator. A d score is defined as<br>
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D=-96.6DΔ/L+18.6T-116.9    (2)<br>
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Here, ΔG is the Gibbs free energy change of stemloop formation. L is the length of stemloop. T is the score of T tail.
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</p>
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<p>To get a relationship between d score and efficiency, we use the biofab data as
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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).</p>
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<img src=" http://2012.igem.org/wiki/images/d/db/Result-1.png" alt="" class="change" />
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(Figure 1 diagram showing the correlation between d score and efficiency)
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<p><img src="http://2012.igem.org/wiki/images/0/0d/%E6%97%A0%E6%A0%87%E9%A2%9821.png" width="880" height="500"class="img_fl img_border" /></p>
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<p>We found that d score and efficiency is positively correlated. Linear fitting is
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performed and the fitting curve is<br>
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E=1.4D+39.1  (2)<br>
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The R^2 is 0.54.</p>
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<p>We proposed that terminators can be classified into three classes based on efficiency.
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<img src=" http://2012.igem.org/wiki/images/7/78/Result-2.JPG" alt="" class="change" />
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(Table.1 Table of  efficiency and d score correspond to different class of terminators).
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<h3>2, Validating theoretical model by existing data</h3>
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<p>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 (Fig 2). We found that our theoretical predication fit experiemental data quite well with correlation coefficient 0.8
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<img src=" http://2012.igem.org/wiki/images/4/48/Result-3.png" alt="" class="change" />
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(Figure 2, diagram of validation using our experimental data)</p>
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<h3>3, TTEC software and webtool</h3>
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<p>We developed TTEC software to predict terminator efficiency, which is available at
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www.terminator efficiency.com                            (for our web tool)<br>
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https://github.com/igemsoftware/SUSTC_Shenzhen_B_2012    (for our software)<br>
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<img src=" http://2012.igem.org/wiki/images/5/59/Result-4.png" alt="" class="change" />
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(Figure 4 the interface of our web tool)
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<img src="  http://2012.igem.org/wiki/images/3/3a/Result-5.png" alt="" class="change" />
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(Figure 5 the intrface of outr software)</p>
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<h3>4, Database of terminator efficiency</h3>
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<p>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.
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<img src="http://2012.igem.org/wiki/images/3/37/Result-6.png " alt="" class="change" />
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(Figure 6 our database of terminators whose efficiency have been measured)</p>
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<br>  

Revision as of 23:00, 26 October 2012

Title

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 (Fig 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 4 the interface of our web tool) (Figure 5 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 6 our database of terminators whose efficiency have been measured)


South University of Science and Technology of China