Team:SUSTC-Shenzhen-B/achievements

From 2012.igem.org

(Difference between revisions)
 
(16 intermediate revisions not shown)
Line 395: Line 395:
                         <ul id="topnav" class="sf-menu">
                         <ul id="topnav" class="sf-menu">
                             <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Home</a></li>
                             <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B">Home</a></li>
 +
                            <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/project.overview">Project Overview</a></li>
                             <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Software</a>
                             <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Software</a>
                             <ul>
                             <ul>
-
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Overview</a></li>
+
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/introduction">Overview</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/algorithm">Algorithm</a></li>
-
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Achievements</a></li>
+
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/achievements">Results</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">Download</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/Download">Download</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Comment</a></li>
                                     <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/comment">Comment</a></li>
Line 434: Line 435:
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/august">August</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/September">September</a></li>
-
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</a></li>
+
                                    
                               </ul>
                               </ul>
                             </li>
                             </li>
Line 443: Line 444:
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/high.school.visits">High School Visits</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/high.school.visits">High School Visits</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/SynBio.intro">SynBio Intro</a></li>
                                   <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/SynBio.intro">SynBio Intro</a></li>
-
                                  <li><a href="http://2012.igem.org/Team:SUSTC-Shenzhen-B/October">October</a></li>
 
                               </ul>
                               </ul>
                             </li>
                             </li>
Line 449: Line 449:
                     </nav><!-- nav -->
                     </nav><!-- nav -->
                      
                      
-
                    <ul id="sn">
+
                 
-
                    <li><a href="http://twitter.com" title="Twitter"><span class="icon-img" style="background:url(/wiki/images/1/1a/Sustc-b1-social-twitter.png)"></span></a></li>
+
-
                        <li><a href="http://plus.google.com" title="Google+"><span class="icon-img" style="background:url(/wiki/images/7/70/Sustc-b1-social-google.png)"></span></a></li>
+
-
                        <li><a href="http://facebook.com" title="Facebook"><span class="icon-img" style="background:url(/wiki/images/a/a7/Sustc-b1-social-facebook.png)"></span></a></li>
+
-
                        <li><a href="http://pinterest.com" title="pinterest"><span class="icon-img" style="background:url(/wiki/images/b/bb/Sustc-b1-social-pinterest.png)"></span></a></li>
+
-
                    </ul>
+
                     <div class="clear"></div>
                     <div class="clear"></div>
                 </section>
                 </section>
Line 470: Line 465:
              
              
<article>
<article>
-
<h2><p>Achievements</p></h2>
+
<h1><p>Results</p></h1>
-
                 <h3 class="STYLE13">1. Function of our Web Tool and PC Software</h3>
+
                 <h3>1. Theoretical model of predicting efficiency of terminators</h3>
-
<p>If the user input his terminator sequence, our program will output the secondary structure of the terminator based on Energy Minimization Rule and the termination efficiency.  There is a database we make which includes many efficiency-measured terminators and some basic information of those terminators.</p>
+
-
<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" />
+
-
<h3 class="STYLE13">2. Calculation of Terminator Efficiency</h3>
+
-
<p>We calculate the d score of 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 linear fitting and the R^2 is 0.54. The picture below shows the results:</p><p>
+
-
<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>
+
-
<br>
+
-
<p>(Figure 1:The x-axis is d score and the y-axis is termination  efficiency)</p>
+
-
<p>Our lab group did  experiments to measured 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 of 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>
+
-
<p>
+
-
<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>
+
-
<p>(Figure 2)</p>
+
-
<p>We thought the results were  good but we would continue to better our prediction in future.</p>
+
-
<h3 class="STYLE13">3. Our Database</h3>
+
-
<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 so 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 so it will be more useful for people. </p>
+
<p>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<br>
 +
D=-96.6DΔG/L+18.6T-116.9    (1)<br>
 +
Here, ΔG is the Gibbs free energy change of stemloop formation. L is the length of stemloop. T is the score of T tail.
 +
</p>
 +
<p>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).</p>
 +
<img src="http://2012.igem.org/wiki/images/0/0e/Result-7.png" alt="" class="change" /><br>
 +
(Figure 1 diagram showing the correlation between d score and efficiency)
-
<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>
+
<p>We found that d score and efficiency is positively correlated. Linear fitting by parts is performed.
 +
We calculate the average error as follows:<br>
 +
<img src="http://2012.igem.org/wiki/images/6/6d/Result-8.1.JPG" alt="" class="change" />     (2)<br>
 +
Here Δe is the average error, n is the number of data , E(prediction) is the efficiency predicted by our model and  E(measurement) is the efficiency measured in experiment.<br>
 +
For Figure 1, the average error is 16%.
 +
 +
<p>We proposed that terminators can be classified into three classes based on efficiency.<br>
 +
<img src="http://2012.igem.org/wiki/images/7/77/Result-9.JPG" alt="" class="change" /><br>
 +
(Table.1 Table of  efficiency and d score correspond to different class of terminators).
 +
 +
<h3>2, Validating theoretical model by our own experimental data</h3>
 +
 +
<p>We did experiment to measure the efficiency of terminators.Using the experimental data, we plot the predicted efficiency based on our model with efficiency data (Figure 2). We found that our theoretical predication fit experiemental data quite well.<br>
 +
<img src=" http://2012.igem.org/wiki/images/a/a5/Result-10.png" alt="" class="change" /><br>
 +
(Figure 2, diagram of validation using our experimental data)</p><br>
 +
<p>For Figure 2, we also calculate the average error. using equation(2).  The result is 18%.</p>
 +
<h3>3, TTEC software and webtool</h3>
 +
<p>We developed TTEC software to predict terminator efficiency, which is available at
 +
www.terminator efficiency.com                            (for our web tool)<br>
 +
https://github.com/igemsoftware/SUSTC_Shenzhen_B_2012    (for our software)<br>
 +
<img src=" http://2012.igem.org/wiki/images/5/59/Result-4.png" alt="" class="change" /><br>
 +
(Figure 3 the interface of our web tool)<br>
 +
<img src="  http://2012.igem.org/wiki/images/3/3a/Result-5.png" alt="" class="change" /><br>
 +
(Figure 4 the intrface of outr software)</p>
 +
<h3>4, Database of terminator efficiency</h3>
 +
<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.
 +
<img src="http://2012.igem.org/wiki/images/3/37/Result-6.png " alt="" class="change" /><br>
 +
(Figure 5 our database of terminators whose efficiency have been measured)</p>
<br>  
<br>  
                 </article>
                 </article>
-
 
-
<div class="col col13 no_margin_right">
 
-
                <h2><p>Explanations</p></h2>
 
-
                <img src="http://2012.igem.org/wiki/images/e/e9/Transcription.jpg" alt="" class="img_fl img_border" /> 
 
-
<p>The process of transcription</p>
 
-
<br>
 
-
                <img src="http://2012.igem.org/wiki/images/1/15/Second_structure.JPG " alt="" class="img_fl img_border" />
 
-
<p>the secondary structure of terminator</p>
 
-
 
                  
                  
                 <div class="clear"></div>
                 <div class="clear"></div>

Latest revision as of 04:01, 27 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=-96.6DΔG/L+18.6T-116.9 (1)
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 by parts is performed. We calculate the average error as follows:
(2)
Here Δe is the average error, n is the number of data , E(prediction) is the efficiency predicted by our model and E(measurement) is the efficiency measured in experiment.
For Figure 1, the average error is 16%.

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 our own experimental data

We did experiment to measure the efficiency of terminators.Using the experimental data, we plot the predicted efficiency based on our model with efficiency data (Figure 2). We found that our theoretical predication fit experiemental data quite well.

(Figure 2, diagram of validation using our experimental data)


For Figure 2, we also calculate the average error. using equation(2). The result is 18%.

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)


South University of Science and Technology of China